UPDio
R Dependencies
quantsmooth
ggplot2
Perl Dependencies
Statistics::R (0.31)
Path::Class
Vcf
Iterator::Simple
List::MoreUtils
Math::Round
Const::Fast
UPDio was tested using R version 2.14.1
One script is missing in version 1.0
cp ~/UPDio/version_0.9/scripts/plot_zygosity_and_events.R ~/UPDio/version_1.0/scripts/
Pre-processing data
for i in /ifs/data/research/projects/kevin/UPD/VCFtest/*.vcf; do cat $i | perl -I "/ifs/home/kevin/perl5/lib/perl5/" ../scripts/sort-vcf | bgzip > $(basename "$i" | cut -d_ -f1).sorted.vcf.gz ; perl -I "/ifs/home/kevin/perl5/lib/perl5/" ../scripts/add_hom_refs_to_vcf.pl --polymorphic_sites ../sample_data/common_variants_within_well_covered_target_regions.txt --no_homREF_vcf $(basename "$i" | cut -d_ -f1).sorted.vcf.gz | bgzip > $(basename "$i" | cut -d_ -f1).sorted.homREFed.vcf.gz ; done
Get CNV
for i in /ifs/data/diagnostics/nextseq/exomes/work/DNA*/GRCh37_*/CNVCalling*_conifer/*_calls.txt ; do cp -n $i /ifs/data/research/projects/kevin/UPD/CNV ; done
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA*/GRCh37_*/CNVCalling*_conifer/*_calls.txt ; do cp -n $i /ifs/data/research/projects/kevin/UPD/CNV ; done
### Select sample to use CNV
for i in $(cat /ifs/data/research/projects/kevin/UPD/results/compare/upd_called.txt) ; do cp -n /ifs/data/research/projects/kevin/UPD/CNV/$(echo $i)_calls.txt /ifs/data/research/projects/kevin/UPD/CNV_pub ; done
for i in $(cat /ifs/data/research/projects/kevin/UPD/results/compare/upd_called.txt) ; do grep $i /ifs/data/research/projects/kevin/UPD/FamilyInformation_sorted.txt >> /ifs/data/research/projects/kevin/UPD/FamilyInformation_sorted_UPD_wo_CNV.txt ; done
for i in /ifs/data/research/projects/kevin/UPD/CNV_pub/*calls.txt ; do tail -n+2 $i | cut -f2,3,4 > /ifs/data/research/projects/kevin/UPD/CNV_pub/$(basename $i | cut -d_ -f1).cnv.txt ; done
Run UPDio
perl -I "/ifs/home/kevin/perl5/lib/perl5/" UPDio.pl --child_vcf /ifs/home/kevin/UPDio/version_1.0/pre_processing/DNA18-03831B.sorted.homREFed.vcf.gz --mom_vcf /ifs/home/kevin/UPDio/version_1.0/pre_processing/DNA18-03833B.sorted.homREFed.vcf.gz --dad_vcf /ifs/home/kevin/UPDio/version_1.0/pre_processing/DNA18-03832B.sorted.homREFed.vcf.gz --path_to_R /cm/shared/apps/bioinf/R/3.5.1/bin/R --R_scripts_dir /ifs/home/kevin/UPDio/version_1.0/scripts --include_MI --common_cnv_file /ifs/home/kevin/UPDio/version_1.0/sample_data/common_dels_1percent.tsv --increase_cnv_filtering --child_cnv_data /ifs/home/kevin/UPDio/version_1.0/pre_processing/DNA18-03831B_cnv.txt
perl -I "/ifs/home/kevin/perl5/lib/perl5/" UPDio.pl --child_vcf /ifs/home/kevin/UPDio/version_1.0/pre_processing/DNA11-26540B.sorted.homREFed.vcf.gz --mom_vcf /ifs/home/kevin/UPDio/version_1.0/pre_processing/DNA12-07537B.sorted.homREFed.vcf.gz --dad_vcf /ifs/home/kevin/UPDio/version_1.0/pre_processing/DNA12-07536B.sorted.homREFed.vcf.gz --path_to_R /cm/shared/apps/bioinf/R/3.5.1/bin/R --R_scripts_dir /ifs/home/kevin/UPDio/version_1.0/scripts
Two loops that rule them all
## PREPROCESSING LOOP
for i in /ifs/data/research/projects/kevin/UPD/VCF/*.vcf; do cat $i | perl -I "/ifs/home/kevin/perl5/lib/perl5/" /ifs/home/kevin/UPDio/version_1.0/scripts/sort-vcf | bgzip > /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(basename "$i" | cut -d_ -f1).sorted.vcf.gz ; perl -I "/ifs/home/kevin/perl5/lib/perl5/" /ifs/home/kevin/UPDio/version_1.0/scripts/add_hom_refs_to_vcf.pl --polymorphic_sites /ifs/home/kevin/UPDio/version_1.0/sample_data/common_variants_within_well_covered_target_regions.txt --no_homREF_vcf /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(basename "$i" | cut -d_ -f1).sorted.vcf.gz | bgzip > /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(basename "$i" | cut -d_ -f1).sorted.homREFed.vcf.gz ; rm -f /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(basename "$i" | cut -d_ -f1).sorted.vcf.gz ; done
## UPDio LOOP
for i in $(cat < "/ifs/data/research/projects/kevin/UPD/family_sorted_mendel.txt") ; do IFS=$'\n' ; perl -I "/ifs/home/kevin/perl5/lib/perl5/" UPDio.pl --child_vcf /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(echo $i | cut -f2).sorted.homREFed.vcf.gz --mom_vcf /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(echo $i | cut -f4).sorted.homREFed.vcf.gz --dad_vcf /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(echo $i | cut -f3).sorted.homREFed.vcf.gz --path_to_R /cm/shared/apps/bioinf/R/3.5.1/bin/R --R_scripts_dir /ifs/home/kevin/UPDio/version_1.0/scripts --output_path ifs/data/research/projects/kevin/UPD/VCF_UPDio_processed --include_MI --common_cnv_file /ifs/home/kevin/UPDio/version_1.0/sample_data/common_dels_1percent.tsv ; done
Plot legend
BPI = Biparental
UA = Uniparental Ambigous
UI = Uniparental Isodisomic
Informative genotype combinations. Sites at which parents are opposing homozygotes
and the child is heterozygous are diagnostic of biparental inheritance. Uniparental
inheritance combinations include those that obligately result from isodisomy (UI), and
those that may result from either heterodisomy or isodisomy (UA) as the proband
alleles may have arisen from a duplication of one parental homolog, or may present
both homologs. True isodisomy events will have mixtures of both of these informative
types, while true heterodisomy events will be void of UI types.
Create a file with all data
for i in /ifs/data/research/projects/kevin/UPD/VCF_UPDio_processed/*upd; do awk '{print FILENAME (NF?"\t":"") $0}' $i | sed 's/.sorted.homREFed.upd//g' >> /ifs/data/research/projects/kevin/UPD/VCF_UPDio_processed/complete_UPD.tsv ; done
Specific analysis with trio for publication
sed 's/\t.\{5\}/&-/g' FamilyInformation.txt | sed '/^ /d' | sed '/^?/d' | sort -n > FamilyInformation_sorted.txt
for i in $(cat < "/ifs/data/research/projects/kevin/UPD/FamilyInformation_sorted.txt") ; do IFS=$'\n' ; perl -I "/ifs/home/kevin/perl5/lib/perl5/" /ifs/home/kevin/UPDio/version_1.0/UPDio.pl --child_vcf /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(echo $i | cut -f2).sorted.homREFed.vcf.gz --mom_vcf /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(echo $i | cut -f4).sorted.homREFed.vcf.gz --dad_vcf /ifs/data/research/projects/kevin/UPD/VCF_UPDio/$(echo $i | cut -f3).sorted.homREFed.vcf.gz --path_to_R /cm/shared/apps/bioinf/R/3.5.1/bin/R --R_scripts_dir /ifs/home/kevin/UPDio/version_1.0/scripts --output_path ifs/data/research/projects/kevin/UPD/VCF_UPDio_processed_pub --include_MI --common_cnv_file /ifs/home/kevin/UPDio/version_1.0/sample_data/common_dels_1percent.tsv ; done
## UPDio loop
sh loop.sh
## UPDio loop for UPD with CNV data
sh loop_w_cnv.sh
## file with all data
for i in /ifs/data/research/projects/kevin/UPD/VCF_UPDio_processed_pub/*upd; do awk '{print FILENAME (NF?"\t":"") $0}' $i | sed 's/.sorted.homREFed.upd//g' | sed 's/\/ifs\/data\/research\/projects\/kevin\/UPD\/VCF_UPDio_processed_pub\///g' >> /ifs/data/research/projects/kevin/UPD/VCF_UPDio_processed_pub/complete_UPD.tsv ; done
## file with all data + cnv
for i in /ifs/data/research/projects/kevin/UPD/VCF_UPDio_processed_pub_cnv/*upd; do awk '{print FILENAME (NF?"\t":"") $0}' $i | sed 's/.sorted.homREFed.upd//g' | sed 's/\/ifs\/data\/research\/projects\/kevin\/UPD\/VCF_UPDio_processed_pub_cnv\///g' >> /ifs/data/research/projects/kevin/UPD/VCF_UPDio_processed_pub_cnv/complete_UPD_pub_cnv.tsv ; done
## COPY png
for i in /ifs/data/research/projects/kevin/UPD/VCF_UPDio_processed_pub/*png; do cp -n $i /ifs/data/research/projects/kevin/UPD/results_png ; done
## Compare with ROH
for i in $(cat results/ROH_complete_iso.txt) ; do ls VCF_UPDio_processed_pub | grep $i ; done
Selected UPD from 4912 trio
### list of all samples
15:43:28 kevin::login03 { ~/UPD/data/Whole/VCF_UPDio_processed_cnv }-> ls *.upd | cut -f1 -d. > allsamples.txt
### list of selected upd
11:34:25 kevin::login03 { ~/UPD/data/Whole/results_png }-> ls | grep -f selectedupd.txt > selectedupd_filename.txt
11:34:51 kevin::login03 { ~/UPD/data/Whole/results_png }-> mkdir selected
11:35:10 kevin::login03 { ~/UPD/data/Whole/results_png }-> cat selectedupd_filename.txt | xargs -I % cp % selected/
### get H3M2 plot of selected upd
while read -r line; do
cp -n /ifs/data/diagnostics/bgi/exomes/work/${line}/GRCh37_*/ROH_*/*.pdf selected/
cp -n /ifs/data/diagnostics/nextseq/exomes/work/${line}/GRCh37_*/ROH_*/*.pdf selected/
done < selectedupd.txt
### get MAD score only for UPDIO trio
15:49:46 kevin::login03 { ~/UPD/data/Whole/VCF_UPDio_processed_cnv }-> head -n1 ../results/allROH_processed.tsv > trioupdioROH_processed_MADscore.tsv
15:51:07 kevin::login03 { ~/UPD/data/Whole/VCF_UPDio_processed_cnv }-> grep -f ~/UPD/data/Whole/VCF_UPDio_processed_cnv/allsamples.txt ../results/allROH_processed_MADscore_quality.tsv >> trioupdioROH_processed_MADscore.tsv
Prepare data for mendelian concordance analysis
### Prepare file with child and parents name
16:06:46 kevin::login03 { ~/UPD/data/Whole }-> sed "s/.\{5\}/&-/" family.txt | sed 's/\t.\{5\}/&-/g' | sed '/^ /d' | sed '/^?/d' | sed '1d' | sort | sed '1d' > family_sorted.txt
### Fit for PED format in excel and remove duplicate: family_sorted_mendel.txt
### Remove double -- : sed -i 's/--/-/g' family_sorted_mendel.txt
### Remove duplicate
17:38:36 kevin::login01 { ~/UPD/data/Whole }-> uniq /ifs/data/research/projects/kevin/UPD/child_sorted.txt > /ifs/data/research/projects/kevin/UPD/child_sorted_uniq.txt
### Create PED for each family
for i in $(cat < "/ifs/data/research/projects/kevin/UPD/child_sorted_uniq.txt") ; do grep "$i" /ifs/data/research/projects/kevin/UPD/family_sorted_mendel.txt > /ifs/data/research/projects/kevin/UPD/VCFtools/$(echo "$i").mendel; done
### Copy all needed VCF
for i in /ifs/data/diagnostics/nextseq/exomes/work/DNA*/GRCh37_*/SNVC*/*.vcf* ; do cp -n $i /ifs/data/research/projects/kevin/UPD/VCF ; done
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA*/GRCh37_*/SNVC*/*.vcf* ; do cp -n $i /ifs/data/research/projects/kevin/UPD/VCF ; done
Merge VCF
### Create new folder with fitted for merge VCF
cp -r /ifs/data/research/projects/kevin/UPD/VCF /ifs/data/research/projects/kevin/UPD/VCF_MC
for file in *haplotypecaller*; do mv "$file" "${file/_haplotypecaller/}" ; done
for file in *unifiedgenotyper*; do mv "$file" "${file/_unifiedgenotyper/}" ; done
## Add - for DNA names in VCF
for i in /ifs/data/research/projects/kevin/UPD/VCF_MC ; do sed -i "s/FORMAT\t.\{5\}/&-/" $i ; sed -i 's/--/-/g' $i ; done
### Merge in VCFmerge folder
mkdir /ifs/data/research/projects/kevin/UPD/VCFmerge/
for i in $(cat < "/ifs/data/research/projects/kevin/UPD/family_sorted_mendel.txt") ; do IFS=$'\n' ; bcftools merge -o /ifs/data/research/projects/kevin/UPD/VCFmerge/$(echo $i | cut -f2)_merged.vcf -O v -m none /ifs/data/research/projects/kevin/UPD/VCF_MC/$(echo $i | cut -f2).vcf /ifs/data/research/projects/kevin/UPD/VCF_MC/$(echo $i | cut -f3).vcf /ifs/data/research/projects/kevin/UPD/VCF_MC/$(echo $i | cut -f4).vcf ; done
Copy all data
for i in /ifs/data/diagnostics/nextseq/exomes/work/DNA*/GRCh37_*/SNVC*/SNVA*/SNVD*/*mendelian_inheritance.txt ; do cp -n $i /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_raw ; done
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA*/GRCh37_*/SNVC*/SNVA*/SNVD*/*mendelian_inheritance.txt ; do cp -n $i /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_raw ; done
Get processable data for z-score. Beware : I had a one issue from DNA17-06937B_mendelian_inheritance.txt as no variant in chrX were inherited from the father.
### Remove chrY and chrM since they have 0 and we can't divide by zero
for i in /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_raw/*_mendelian_inheritance.txt; do sed -i '/chrY/d' $i ; sed -i '/chrM/d' $i ; done
### Remove header line
for i in /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_raw/*_mendelian_inheritance.txt; do sed -i '1d' $i ; done
### Get data.frame for maternal UPD
for i in /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_raw/*mendelian_inheritance.txt ; do printf "Sample\n$(basename "$i" | cut -d_ -f1)" > /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3/$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
### Get data.frame for paternal UPD
for i in /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_raw/*mendelian_inheritance.txt ; do printf "Sample\n$(basename "$i" | cut -d_ -f1)" > /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_paternal_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($2/$3)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_paternal_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_paternal_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_paternal_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
Create complete dataset with all patients
### maternal
head -n1 /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/DNA18-16505B_mendelian_inheritance.processed.bed > /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/all_mendelian_inheritance_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> all_mendelian_inheritance_processed.tsv
### paternal
head -n1 /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/DNA18-16505B_mendelian_inheritance.processed.bed > /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_paternal_processed/all_mendelian_inheritance_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_paternal_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> all_mendelian_inheritance_processed.tsv
Create z-score and column for filtering
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/all_mendelian_inheritance_processed.tsv
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_paternal_processed/all_mendelian_inheritance_processed.tsv
Add column for filtering
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/all_mendelian_inheritance_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_processed/all_mendelian_inheritance_processed_zscore_quality.tsv
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_paternal_processed/all_mendelian_inheritance_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/mendelian_inheritance_paternal_processed/all_mendelian_inheritance_paternal_processed_zscore_quality.tsv
Filter file with =< X chromosome under 2
### ALL
cut -f1-24 all_mendelian_inheritance_paternal_processed_zscore_quality.tsv > all_mendelian_inheritance_paternal_processed_zscore_quality_R.tsv
cut -f1-24 all_mendelian_inheritance_maternal_processed_zscore_quality.tsv > all_mendelian_inheritance_maternal_processed_zscore_quality_R.tsv
### P1
head -n1 all_mendelian_inheritance_paternal_processed_zscore_quality.tsv > all_mendelian_inheritance_paternal_processed_zscore_quality_1.tsv
tail -n+2 all_mendelian_inheritance_paternal_processed_zscore_quality.tsv | awk -F "\t" '$(NF-3) == 1 {print $0}' >> all_mendelian_inheritance_paternal_processed_zscore_quality_1.tsv
cut -f1-24 all_mendelian_inheritance_paternal_processed_zscore_quality_1.tsv > all_mendelian_inheritance_paternal_processed_zscore_quality_1_R.tsv
#### M1
head -n1 all_mendelian_inheritance_maternal_processed_zscore_quality.tsv > all_mendelian_inheritance_maternal_processed_zscore_quality_1.tsv
tail -n+2 all_mendelian_inheritance_maternal_processed_zscore_quality.tsv | awk -F "\t" '$(NF-3) == 1 {print $0}' >> all_mendelian_inheritance_maternal_processed_zscore_quality_1.tsv
cut -f1-24 all_mendelian_inheritance_maternal_processed_zscore_quality_1.tsv > all_mendelian_inheritance_maternal_processed_zscore_quality_1_R.tsv
### P2
head -n1 all_mendelian_inheritance_paternal_processed_zscore_quality.tsv > all_mendelian_inheritance_paternal_processed_zscore_quality_2.tsv
tail -n+2 all_mendelian_inheritance_paternal_processed_zscore_quality.tsv | awk -F "\t" '$(NF-3) <= 2 && $(NF-3) > 0 {print $0}' >> all_mendelian_inheritance_paternal_processed_zscore_quality_2.tsv
cut -f1-24 all_mendelian_inheritance_paternal_processed_zscore_quality_2.tsv > all_mendelian_inheritance_paternal_processed_zscore_quality_2_R.tsv
#### M2
head -n1 all_mendelian_inheritance_maternal_processed_zscore_quality.tsv > all_mendelian_inheritance_maternal_processed_zscore_quality_2.tsv
tail -n+2 all_mendelian_inheritance_maternal_processed_zscore_quality.tsv | awk -F "\t" '$(NF-3) <= 2 && $(NF-3) > 0 {print $0}' >> all_mendelian_inheritance_maternal_processed_zscore_quality_2.tsv
cut -f1-24 all_mendelian_inheritance_maternal_processed_zscore_quality_2.tsv > all_mendelian_inheritance_maternal_processed_zscore_quality_2_R.tsv
R
Number of samples :
15:59:10 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA13-*/GRCh37_*/ROH_*/*.bed | wc -l
2741
16:00:10 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA12-*/GRCh37_*/ROH_*/*.bed | wc -l
904
16:00:49 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA11-*/GRCh37_*/ROH_*/*.bed | wc -l
382
16:01:02 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA10-*/GRCh37_*/ROH_*/*.bed | wc -l
253
16:01:12 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA09-*/GRCh37_*/ROH_*/*.bed | wc -l
178
16:01:21 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA08-*/GRCh37_*/ROH_*/*.bed | wc -l
115
16:01:28 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA07-*/GRCh37_*/ROH_*/*.bed | wc -l
55
16:01:33 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA06-*/GRCh37_*/ROH_*/*.bed | wc -l
63
16:01:38 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA05-*/GRCh37_*/ROH_*/*.bed | wc -l
45
16:01:43 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA03-*/GRCh37_*/ROH_*/*.bed | wc -l
16
16:01:47 kevin::login03 { ~ }-> ls -f /ifs/data/diagnostics/bgi/exomes/work/DNA02-*/GRCh37_*/ROH_*/*.bed | wc -l
7
15:40:35 kevin::login02 { /ifs/data/research/projects/kevin/UPD/results }-> ls /ifs/data/diagnostics/nextseq/exomes/work/DNA*/GRCh37_*/ROH_*/*.bed | wc -l
594
Get name for proband
for i in /ifs/data/diagnostics/nextseq/exomes/work/DNA*/GRCh37_*/*.properties; do grep "family_fraction_numbers" $i >> /ifs/data/research/projects/kevin/UPD/samples.txt ; done
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA*/GRCh37_*/*.properties; do grep "family_fraction_numbers" $i >> /ifs/data/research/projects/kevin/UPD/samples.txt ; done
17:05:51 kevin::login02 { /ifs/data/research/projects/kevin/UPD }-> sort samples.txt | uniq | sed 's/family_fraction_numbers=//g' | sed 's/;/\t/g' | sed 's/\\//g' | sed 's/KIND://g' | sed 's/VADER://g' | sed 's/MOEDER://g' >> family.txt
#### split
tail -n +2 /ifs/data/research/projects/kevin/UPD/family.txt | cut -f1 > /ifs/data/research/projects/kevin/UPD/child.txt
tail -n +2 /ifs/data/research/projects/kevin/UPD/family.txt | cut -f2 > /ifs/data/research/projects/kevin/UPD/father.txt
tail -n +2 /ifs/data/research/projects/kevin/UPD/family.txt | cut -f3 > /ifs/data/research/projects/kevin/UPD/mother.txt
17:31:31 kevin::login02 { /ifs/data/research/projects/kevin/UPD }-> sed -i -e "s/.\{5\}/&-/" child.txt
17:32:05 kevin::login02 { /ifs/data/research/projects/kevin/UPD }-> sed -i -e "s/.\{5\}/&-/" father.txt
17:32:18 kevin::login02 { /ifs/data/research/projects/kevin/UPD }-> sed -i -e "s/.\{5\}/&-/" mother.txt
17:36:39 kevin::login02 { /ifs/data/research/projects/kevin/UPD }-> sort child.txt | sed '/^ /d' | sed '/^?/d' | sed '1d' > child_sorted.txt
17:39:33 kevin::login02 { /ifs/data/research/projects/kevin/UPD }-> sort father.txt | sed '/^ /d' | sed '/^?/d' | sed '1d' > father_sorted.txt
17:39:41 kevin::login02 { /ifs/data/research/projects/kevin/UPD }-> sort mother.txt | sed '/^ /d' | sed '/^?/d' | sed '1d' > mother_sorted.txt
Copy all ROH file done from known data
###### Home
for i in /ifs/data/diagnostics/nextseq/exomes/work/DNA*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/nextseq_raw/ ; done
###### BGI
## before 2012
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA0*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/before2012_ROH_raw/ ; done
DNA0*/GRCh37_*/ROH_*/*.bed
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA10-*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/before2012_ROH_raw/ ; done
DNA10*/GRCh37_*/ROH_*/*.bed
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA11-*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/before2012_ROH_raw/ ; done
DNA1*/GRCh37_*/ROH_*/*.bed
## after 2012
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA12-*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/2012_ROH_raw/ ; done
DNA12*/GRCh37_*/ROH_*/*.bed
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA13-*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/2013_ROH_raw/ ; done
DNA13*/GRCh37_*/ROH_*/*.bed
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA14-*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/2014_ROH_raw/ ; done
DNA14*/GRCh37_*/ROH_*/*.bed
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA15-*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/2015_ROH_raw/ ; done
DNA15*/GRCh37_*/ROH_*/*.bed
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA16-*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/2016_ROH_raw/ ; done
DNA16*/GRCh37_*/ROH_*/*.bed
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA17-*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/2017_ROH_raw/ ; done
DNA17*/GRCh37_*/ROH_*/*.bed
for i in /ifs/data/diagnostics/bgi/exomes/work/DNA18-*/GRCh37_*/ROH_*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/2018_ROH_raw_all/ ; done
DNA18*/GRCh37_*/ROH_*/*.bed
#### ALL
for i in /ifs/data/research/projects/kevin/UPD/*ROH_raw*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/ROH_raw_all/ ; done
for i in /ifs/data/research/projects/kevin/UPD/*nextseq_raw*/*.bed ; do cp -n $i /ifs/data/research/projects/kevin/UPD/ROH_raw_all/ ; done
Get length by chromosome and processable data for z-score calling
### Nextseq
for i in /ifs/data/research/projects/kevin/UPD/nextseq_raw/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/nextseq_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/nextseq_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/nextseq_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/nextseq_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
#### BGI
## Before 2012
for i in /ifs/data/research/projects/kevin/UPD/before2012_ROH_raw/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/before2012_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/before2012_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/before2012_ROH_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/before2012_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
### Since 2012
for i in /ifs/data/research/projects/kevin/UPD/2012_ROH_raw/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/2012_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/2012_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/2012_ROH_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/2012_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
for i in /ifs/data/research/projects/kevin/UPD/2013_ROH_raw/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/2013_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/2013_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/2013_ROH_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/2013_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
for i in /ifs/data/research/projects/kevin/UPD/2014_ROH_raw/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/2014_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/2014_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/2014_ROH_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/2014_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
for i in /ifs/data/research/projects/kevin/UPD/2015_ROH_raw/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/2015_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/2015_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/2015_ROH_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/2015_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
for i in /ifs/data/research/projects/kevin/UPD/2016_ROH_raw/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/2016_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/2016_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/2016_ROH_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/2016_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
for i in /ifs/data/research/projects/kevin/UPD/2017_ROH_raw/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/2017_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/2017_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/2017_ROH_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/2017_ROH_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
for i in /ifs/data/research/projects/kevin/UPD/2018_ROH_raw_all/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/2018_ROH_all_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/2018_ROH_all_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/2018_ROH_all_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/2018_ROH_all_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
### ALL
for i in /ifs/data/research/projects/kevin/UPD/ROH_raw_all/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/ROH_all_processed/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '{l[$1]+=($3-$2)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/ROH_all_processed/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/ROH_all_processed/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/ROH_all_processed/$(basename "$i" | cut -d. -f1).sample.bed ; done
Create whole dataset for all years
#### NextSeq
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/nextseq_processed/nextseq_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/nextseq_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> nextseq_processed.tsv
#### BGI
## Before 2012
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/before2012_ROH_processed/mendelian_inheritance_processed/all_mendelian_inheritance_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/before2012_ROH_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> before2012_allROH_processed.tsv
## After 2012
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/2012_ROH_processed/2012_allROH_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/2012_ROH_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> 2012_allROH_processed.tsv
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/2013_ROH_processed/2013_allROH_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/2013_ROH_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> 2013_allROH_processed.tsv
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/2014_ROH_processed/2014_allROH_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/2014_ROH_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> 2014_allROH_processed.tsv
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/2015_ROH_processed/2015_allROH_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/2015_ROH_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> 2015_allROH_processed.tsv
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/2016_ROH_processed/2016_allROH_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/2016_ROH_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> 2016_allROH_processed.tsv
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/2017_ROH_processed/2017_allROH_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/2017_ROH_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> 2017_allROH_processed.tsv
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/2018_ROH_all_processed/2018_allROH_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/2018_ROH_all_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> 2018_allROH_processed.tsv
### ALL
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/ROH_all_processed/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> allROH_processed.tsv
Jakob tricks and advices : Use SNP, get the biggest and compare.
#### use SNP and get only big ones
11:20:06 kevin::login02 { /ifs/data/research/projects/kevin/UPD/ROH_raw_all }-> for i in *.bed; do cut -f5 $i >> allsnp_number.txt ; done
11:24:29 kevin::login02 { /ifs/data/research/projects/kevin/UPD/ROH_raw_all }-> cat allsnp_number.txt | Rscript -e 'summary (as.numeric (readLines ("stdin")))'
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.0 195.0 259.0 330.7 361.0 36420.0
11:24:50 kevin::login02 { /ifs/data/research/projects/kevin/UPD/ROH_raw_all }-> cat allsnp_number.txt | Rscript -e 'quantile (as.numeric (readLines ("stdin")), probs=c(0.025, 0.5, 0.975))'
2.5% 50% 97.5%
123 259 859
### get for all
for i in /ifs/data/research/projects/kevin/UPD/ROH_raw_all/*.bed ; do printf "Sample\n$(basename "$i" | cut -d. -f1)" > /ifs/data/research/projects/kevin/UPD/ROH_all_processed_jg/$(basename "$i" | cut -d. -f1).sample.bed ; awk -F "\t" '$5 > 361 {l[$1]+=($5)} END {for (i in l) {print i,l[i]}}' "$i" | sort -k1,1V | sed 's/ /\t/g' | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' '\t' | paste /ifs/data/research/projects/kevin/UPD/ROH_all_processed_jg/$(basename "$i" | cut -d. -f1).sample.bed - > /ifs/data/research/projects/kevin/UPD/ROH_all_processed_jg/$(basename "$i" | cut -d. -f1).processed.bed ; rm -f /ifs/data/research/projects/kevin/UPD/ROH_all_processed_jg/$(basename "$i" | cut -d. -f1).sample.bed ; done
### Merge
head -n1 /ifs/data/research/projects/kevin/UPD/2018_ROH_processed/DNA18-16523B.processed.bed > /ifs/data/research/projects/kevin/UPD/ROH_all_processed_jg/allROH_processed.tsv
cd /ifs/data/research/projects/kevin/UPD/ROH_all_processed_jg/
find . -name "*.bed" | xargs -n 1 tail -n +2 >> allROH_processed.tsv
## R
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/ROH_all_processed_jg/allROH_processed.tsv
## filter
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/ROH_all_processed_jg/allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/ROH_all_processed_jg/allROH_processed_jg_zscore_quality.tsv
### ALL
cut -f1-24 allROH_processed_jg_zscore_quality.tsv > allROH_processed_jg_zscore_quality_R.tsv
### Filter
#### 2
head -n1 allROH_processed_zscore_quality.tsv > allROH_processed_zscore_quality_filtered_2.tsv
tail -n+2 allROH_processed_jg_zscore_quality.tsv | awk -F "\t" '$(NF-3) <= 2 && $(NF-3) > 0 {print $0}' >> allROH_processed_jg_zscore_quality_filtered_2.tsv
cut -f1-24 allROH_processed_jg_zscore_quality_filtered_2.tsv > allROH_processed_jg_zscore_quality_filtered_2_R.tsv
Get addition size of all ROH by sample
15:56:01 kevin::login03 { ~/UPD/data/Whole/ROH_all_processed }-> awk '{for(i=1;i<=NF;i++) t+=$i; print $0"\t"t; t=0}' allROH_processed.tsv | cut -f1,26 | sed 's/e\t0/e\tSize/' > allROH_processed_sumsize.tsv
Create z-score and column for filtering
### NextSeq
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/nextseq_processed/nextseq_processed.tsv
### BGI
## Before 2012
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/before2012_ROH_processed/before2012_allROH_processed.tsv
## After 2012
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/2012_ROH_processed/2012_allROH_processed.tsv
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/2013_ROH_processed/2013_allROH_processed.tsv
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/2014_ROH_processed/2014_allROH_processed.tsv
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/2015_ROH_processed/2015_allROH_processed.tsv
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/2016_ROH_processed/2016_allROH_processed.tsv
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/2017_ROH_processed/2017_allROH_processed.tsv
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/2018_ROH_all_processed/2018_allROH_processed.tsv
### ALL
Rscript ~/UPD/zscore.R /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed.tsv
Add column for filtering
### NextSeq
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/nextseq_processed/nextseq_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/nextseq_processed/nextseq_processed_zscore_quality.tsv
### BGI
## Before 2012
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/before2012_ROH_processed/before2012_allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/before2012_ROH_processed/before2012_allROH_processed_zscore_quality.tsv
#### After 2012
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/2012_ROH_processed/2012_allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/2012_ROH_processed/2012_allROH_processed_zscore_quality.tsv
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/2013_ROH_processed/2013_allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/2013_ROH_processed/2013_allROH_processed_zscore_quality.tsv
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/2014_ROH_processed/2014_allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/2014_ROH_processed/2014_allROH_processed_zscore_quality.tsv
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/2015_ROH_processed/2015_allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/2015_ROH_processed/2015_allROH_processed_zscore_quality.tsv
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/2016_ROH_processed/2016_allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/2016_ROH_processed/2016_allROH_processed_zscore_quality.tsv
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/2017_ROH_processed/2017_allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/2017_ROH_processed/2017_allROH_processed_zscore_quality.tsv
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/2018_ROH_all_processed/2018_allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/2018_ROH_all_processed/2018_allROH_processed_zscore_quality.tsv
### ALL
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_zscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_zscore_quality.tsv
15:40:00 kevin::login02 { /ifs/data/research/projects/kevin/UPD }-> for i in */*quality.tsv ; do cp $i results/ ; done
Split for child, father and mother sample
tail -n +2 /ifs/data/research/projects/kevin/UPD/results/allROH_processed_zscore_quality.tsv | sort > /ifs/data/research/projects/kevin/UPD/results/allROH_processed_zscore_quality_sorted.tsv
head -n1 /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_zscore_quality.tsv > /ifs/data/research/projects/kevin/UPD/results/child_allROH_processed_zscore_quality.tsv
grep -f /ifs/data/research/projects/kevin/UPD/child_sorted.txt /ifs/data/research/projects/kevin/UPD/results/allROH_processed_zscore_quality_sorted.tsv >> /ifs/data/research/projects/kevin/UPD/results/child_allROH_processed_zscore_quality.tsv
head -n1 /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_zscore_quality.tsv > /ifs/data/research/projects/kevin/UPD/results/father_allROH_processed_zscore_quality.tsv
grep -f /ifs/data/research/projects/kevin/UPD/father_sorted.txt /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_zscore_quality.tsv >> /ifs/data/research/projects/kevin/UPD/results/father_allROH_processed_zscore_quality.tsv
head -n1 /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_zscore_quality.tsv > /ifs/data/research/projects/kevin/UPD/results/mother_allROH_processed_zscore_quality.tsv
grep -f /ifs/data/research/projects/kevin/UPD/mother_sorted.txt /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_zscore_quality.tsv >> /ifs/data/research/projects/kevin/UPD/results/mother_allROH_processed_zscore_quality.tsv
Filter file with =< X chromosome under 2
### ALL
cut -f1-24 allROH_processed_zscore_quality.tsv > allROH_processed_zscore_quality_R.tsv
### >2 - 1
head -n1 allROH_processed_zscore_quality.tsv > allROH_processed_zscore_quality_filtered_1.tsv
tail -n+2 allROH_processed_zscore_quality.tsv | awk -F "\t" '$(NF-3) == 1 {print $0}' >> allROH_processed_zscore_quality_filtered_1.tsv
cut -f1-24 allROH_processed_zscore_quality_filtered_1.tsv > allROH_processed_zscore_quality_filtered_1_R.tsv
#### >2 - 2
head -n1 allROH_processed_zscore_quality.tsv > allROH_processed_zscore_quality_filtered_2.tsv
tail -n+2 allROH_processed_zscore_quality.tsv | awk -F "\t" '$(NF-3) <= 2 && $(NF-3) > 0 {print $0}' >> allROH_processed_zscore_quality_filtered_2.tsv
cut -f1-24 allROH_processed_zscore_quality_filtered_2.tsv > allROH_processed_zscore_quality_filtered_2_R.tsv
### > 1.5 and 2- 1
head -n1 allROH_processed_zscore_quality.tsv > allROH_processed_zscore_quality_filtered_1.5.tsv
tail -n+2 allROH_processed_zscore_quality.tsv | awk -F "\t" '$(NF-4) == 1 {print $0}' | awk -F "\t" '$(NF-3) == 1 {print $0}' >> allROH_processed_zscore_quality_filtered_1.5.tsv
cut -f1-24 allROH_processed_zscore_quality_filtered_1.5.tsv > allROH_processed_zscore_quality_filtered_1.5_R.tsv
Create MAD and column for filtering Need the quantable package
### ALL
Rscript ~/UPD/MADscore.R /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed.tsv
### Create columns for filtering
# without median awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_MADscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-1;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-2;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-3;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-4;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_MADscore_quality.tsv
## ALL samples
awk -F "\t" '{if(NR==1) c="Number>1.5"; else for(i=2;i<=NF-1;i++) c+=($i>1.5); print $0,c; c=0}' /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_MADscore.tsv | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>2"; else for(i=2;i<=NF-2;i++) d+=($i>2); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>3"; else for(i=2;i<=NF-3;i++) d+=($i>3); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>4"; else for(i=2;i<=NF-4;i++) d+=($i>4); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | awk -F "\t" '{if(NR==1) d="Number>5"; else for(i=2;i<=NF-5;i++) d+=($i>5); print $0,d; d=0}' | column -t | sed 's/ \+ /\t/g' | sed '1s/^/Sample\t/' > /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_MADscore_quality.tsv
cp /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_MADscore_quality.tsv /ifs/data/research/projects/kevin/UPD/results
## Just publication trio
head -n1 /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_MADscore_quality.tsv > /ifs/data/research/projects/kevin/UPD/ROH_all_processed/pubtrioROH_processed_MADscore_quality.tsv
for i in $( cut -f2 /ifs/data/research/projects/kevin/UPD/FamilyInformation_sorted.txt ); do grep $i /ifs/data/research/projects/kevin/UPD/ROH_all_processed/allROH_processed_MADscore_quality.tsv >> /ifs/data/research/projects/kevin/UPD/ROH_all_processed/pubtrioROH_processed_MADscore_quality.tsv ; done
### Filter file with =< X chromosome under 2
### ALL
cut -f1-24 allROH_processed_MADscore_quality.tsv > allROH_processed_MADscore_quality_R.tsv
#### >2 - 2
head -n1 allROH_processed_MADscore_quality.tsv > allROH_processed_MADscore_quality_filtered_2.tsv
tail -n+2 allROH_processed_MADscore_quality.tsv | awk -F "\t" '$(NF-3) <= 2 && $(NF-3) > 0 {print $0}' >> allROH_processed_MADscore_quality_filtered_2.tsv
cut -f1-24 allROH_processed_MADscore_quality_filtered_2.tsv > allROH_processed_MADscore_quality_filtered_2_R.tsv
#### >3 - 2
head -n1 allROH_processed_MADscore_quality.tsv > allROH_processed_MADscore_quality_filtered_3.tsv
tail -n+2 allROH_processed_MADscore_quality.tsv | awk -F "\t" '$(NF-2) <= 2 && $(NF-2) > 0 {print $0}' >> allROH_processed_MADscore_quality_filtered_3.tsv
cut -f1-23 allROH_processed_MADscore_quality_filtered_3.tsv > allROH_processed_MADscore_quality_filtered_3_R.tsv
### for publication
head -n1 pubtrioROH_processed_MADscore_quality.tsv > pubtrioROH_processed_MADscore_quality_filtered_3.tsv
tail -n+2 pubtrioROH_processed_MADscore_quality.tsv | awk -F "\t" '$(NF-2) <= 2 && $(NF-2) > 0 {print $0}' >> pubtrioROH_processed_MADscore_quality_filtered_3.tsv
cut -f1-23 pubtrioROH_processed_MADscore_quality_filtered_3.tsv > pubtrioROH_processed_MADscore_quality_filtered_3_R.tsv
Good ROH on UPDio
for i in $( cut -f2 /ifs/data/research/projects/kevin/UPD/results/compare/pubtrioROH_med3_2.list ); do grep $i /ifs/data/research/projects/kevin/UPD/results/complete_UPD_pub.tsv >> /ifs/data/research/projects/kevin/UPD/results/compare/pubtrioROH_med3_2.updio.tsv ; done
Good UPDio Isodisomy on ROH
sed -i 's/ \+ /\t/g' complete_UPD_pub_cnv_formerge.tsv
sed -i 's/ /\t/g' complete_UPD_pub_cnv_formerge.tsv
19:14:47 kevin::login04 { ~/UPD/data/Whole/results/compare }-> python merge.py
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