neurogenetics / gwas-pipeline Goto Github PK

Hi,

I was running this command in your pipeline:

sed 's/|//g' missing_haps_1E7.txt > missing_haps_1E7_final.txt
sed: -e expression #1, char 7: unterminated `s' command

head missing_haps_1E7.txt
1:3925928:G:A|1:3929593:T:C
1:4359549:T:C|1:4360122:C:T
1:4359563:C:T|1:4360565:T:C
1:4459761:T:C|1:4461905:C:T
...

Can you please let me know how this sed command should look like?

Thanks
Ana

Hello,

is there is a way to do this whole step with removing related individuals in Plink and how it would look like?

gcta --bfile $FILENAME --make-grm --out GRM_matrix --autosome --maf 0.05
gcta --grm-cutoff 0.125 --grm GRM_matrix --out GRM_matrix_0125 --make-grm
plink --bfile $FILENAME --keep GRM_matrix_0125.grm.id --make-bed --out $FILENAME_relatedness

Thanks
Ana