datngu / lmtag

LmTag is a model based method to find tagSNP in SNP array desgin that maximizes imputation coverage and functional score of tag SNPs

Documents for LmTag

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Update news

09 April 2022: v0.2.0

1. Adding model interaction. Now LmTag supports 2 models:

• The linear option models imputation accuracy of a linear funcion of: Imputation_accuracy ~ LD + MAF_tagSNP + MAF_taggedSNP + distance. This model was used in previous versions.
• The interaction option models imputation accuracy of a linear funcion with interaction term of LD and MAF_taggedSNP: Imputation_accuracy ~ LD + MAF_tagSNP + MAF_taggedSNP + distance + LD:MAF_taggedSNP.

In our experiments, the interaction model provides slightly better performance, but it is not significant. We still recommend users to use the linear model for better intepretbility.

2. User friendly interface.

• We created 2 scripts model_pipeline.sh, and LmTag_pipeline.sh that provide more friendly interface for users.
• We also provide a docker image that can run the LmTag easily.
• Details instructions and tutorials for using the two wrapers and docker image is in the sub-directory: docker.

28 December 2021: v0.1.0

31 August 2021: testing version v0.0.2

• Add tagged marker positions column in output.

30 July 2021: testing version v0.0.1

• Add --vip and --exclude parameters: use to add VIP SNPS list and excluded SNPS list for the program.
• VIP SNPs are prioritized to be selected by the algorithm while excluded SNPs are elimiated from the selection.

NOTE: not sure that all VIP SNPs are selected and all excluded SNPs are excluded because the program weight imputation is the primary factor of choosing SNPs.

23 June 2021: testing version 0.0.0

• First submission

1. Introduction

LmTag is a model based method to find tagSNP in SNP array desgin that maximizes imputation coverage and functional score of tag SNPs. Full details of the method is described in the method manuscript.

Software requirements

LmTag is implemented in R and C++. LmTag requires vcftools, bcftools, minimac3, minimac4, plink for model construction step.

• VCFtools 0.1.17 : https://vcftools.github.io
• bcftools 1.10.2 : https://github.com/samtools/bcftools
• plink1.9 : https://www.cog-genomics.org/plink/
• minimac3 : https://genome.sph.umich.edu/wiki/Minimac3
• minimac4 : https://genome.sph.umich.edu/wiki/Minimac4
• A C++-11 compliant compiler version of GCC (g++ >= 4.8.2)
• R packages version 3.6.0 or latter with data.table package installed.

2. Download and installation

2.1 Download

2.2 Installation

# download the software:
git clone https://github.com/datngu/LmTag.git
## Move to the *LmTag* directory and do configuration for LmTag
cd LmTag
# build the C++ program
make
# export to PATH
export PATH=$PWD/bin:$PATH
cd ..

The installation assumes that vcftools, bcftools, minimac3, minimac4, plink are available and can be call directly from your terminal promt.

If vcftools, bcftools, minimac3, minimac4, plink are not available, please install and add these tools to PATH variable. OTHERWISE, THERE WILL BE ERRORS

3. Input requirement

LmTag require a phased vcf file to perform tag SNP selection with following criteria:

• Only biallelic SNPS are considered.
• MAF are carefully check before runing (recommend to use filltag command by bcftools before input to LmTag pipeline) as LmTag extracts MAF directly from INFO/AF information in vcf file.
• Minimum MAF threshold are pre-determine in vcf filer, so you need to do filtering before providing the file to LmTag pipeline.
• #CHROM should be encoded without 'chr' character.

Other possible input files for LmTag:

• Functional scores of SNPs candidates, typically extracted from the CADD databases [optional]
• List of VIP SNPs - they will be prioritized in tag SNP selection at highest levels; typically SNPs in GWAS catalog or ClinVar databases that you really want to select as tag SNPs [optional]
• List of bad SNPs - they will be tried to exluded in tag SNP selection; typically SNPs in repeated regions or low quality that you don't want selected as tag SNPs [optional]

4. Step by step instruction to run LmTag

4.0 Data reprocessing and compute needed information

Obtain tutorial data:

We provide in this tutorial based on chromosome 10, East Asian population dataset:

• vcf file: https://zenodo.org/record/5807198/files/chr10_EAS.vcf.gz?download=1
• CADD score file: https://zenodo.org/record/5807198/files/chr10_EAS_CADD.txt?download=1
• VIP SNP list: https://zenodo.org/record/5807198/files/VIP_GWAS_CLINVAR_ALL.txt?download=1

Recommended protocol for vcf preprocessing:

Assumed that you have a raw vcf file: chr10_EAS.vcf.gz in your current directory, recommended protocol to prepare vcf file is:

bcftools view chr10_EAS.vcf.gz -m2 -M2 -v snps -Q 0.9999999999:major -q 0.01:minor -e 'ALT="."' | bcftools +fill-tags | sed 's/chr//g' | bgzip > chr10_EAS_processed.vcf.gz

Compute needed information

Now we compute LD with plink v1.9 and extract MAF with bcftools:

# compute LD
mkdir plink
plink --vcf chr10_EAS_processed.vcf.gz \
      --vcf-half-call 'haploid' \
      --make-bed  --const-fid --out ./plink/chr10_EAS_tem_file \
      --threads 1 \
      --memory 2000


plink --bfile ./plink/chr10_EAS_tem_file \
      --r --ld-window-r2 0.2 \
      --ld-window 10000 \
      --ld-window-kb 1000 \
      --out ./plink/chr10_EAS_ld_0.2 \
      --threads 8 \
      --memory 2000

mv ./plink/chr10_EAS_ld_0.2.ld ./
rm -r plink

# extract MAF
echo $'CHR\tPOS\tAF' > chr10_EAS_extracted_AF.txt
bcftools query -f '%CHROM\t%POS\t%AF\n' chr10_EAS_processed.vcf.gz >> chr10_EAS_extracted_AF.txt

4.1 Model construction

4.1.1 build m3vcf reference for imputation

We need to build a reference directory for leave one out cross validation imputation with create_imputation_ref.sh. This step may take very long time because it will generate n reference m3vcf files with n-1 samples. n is number of sample in your vcf.gz file. You may download pre-built reference instead of generate it yourself.

create_imputation_ref.sh -v chr10_EAS_processed.vcf.gz -o chr10_EAS_hg38_high_cov -p 16

NOTE: Pre-built imputation reference panel of populations are available for downloading:

EAS: https://zenodo.org/record/5807198/files/chr10_EAS.tar.gz?download=1

EUR: https://zenodo.org/record/5807198/files/chr10_EUR.tar.gz?download=1

SAS: https://zenodo.org/record/5807198/files/chr10_SAS.tar.gz?download=1

Assumed that you have downloaded chr10_EAS.tar.gz, the upzip command is:

tar -xvzf chr10_EAS.tar.gz

4.1.1 Create naive array and compute imputation accuracy for naive array.

We need to build a naive array to entablish relation between LD, MAF, and distance of SNPs with build_naive_array.R. The idea is to sampling n SNPs uniformlly based on their index after sorting by genomic position. Next, we impute with pre-built imputation reference m3vcf with imputation_with_prebuilt_ref.sh and compute imputaion accuracy with compute_imputation_accuracy.R.

# size=32970 is the size (number of tag SNP selected by obtain by TagIt with the same input vcf file - read main paper for further information).
build_naive_array.R vcf=chr10_EAS_processed.vcf.gz size=32970 out=chr10_EAS_naive.txt

imputation_with_prebuilt_ref.sh -t chr10_EAS_naive.txt -r chr10_EAS_hg38_high_cov -o naive_chr10_EAS -p 16

compute_imputation_accuracy.R imputation=naive_chr10_EAS out=naive_chr10_EAS.Rdata

4.1.2 Find best tagSNP

Finding best tagSNP (belong to chr10_EAS_naive.txt) by LmTag find command for all SNPs.

LmTag find --tag chr10_EAS_naive.txt --ld chr10_EAS_ld_0.2.ld -o chr10_EAS_find_snp_output.txt

4.1.3 Building model with computed inputs

Now we can build model with buid_imputation_model.R

buid_imputation_model.R imputation_Rdata=naive_chr10_EAS.Rdata find_snp=chr10_EAS_find_snp_output.txt out_Rdata=chr10_EAS_model.Rdata

4.2 Tag SNP selection with LmTag

4.2.1 Fitting model to generate input for LmTag

This step need ld file generated by plink v1.9, AF file generated by bcftools, and model build by ./buid_imputation_model.R.

Now LmTag supports 2 models:

• The linear option (model=linear) models imputation accuracy of a linear funcion of: Imputation_accuracy ~ LD + MAF_tagSNP + MAF_taggedSNP + distance. This model was used in previous versions.

fit_imputation_model.R model_Rdata=chr10_EAS_model.Rdata model=linear af=chr10_EAS_extracted_AF.txt ld=chr10_EAS_ld_0.2.ld ld_cutoff=0.8 out_ld=chr10_EAS_ld_fitted_model.txt

• The interaction option (model=interaction) models imputation accuracy of a linear funcion with interaction term of LD and MAF_taggedSNP: Imputation_accuracy ~ LD + MAF_tagSNP + MAF_taggedSNP + distance + LD:MAF_taggedSNP.

fit_imputation_model.R model=interaction model_Rdata=chr10_EAS_model.Rdata af=chr10_EAS_extracted_AF.txt ld=chr10_EAS_ld_0.2.ld ld_cutoff=0.8 out_ld=chr10_EAS_ld_fitted_model.txt

In our experiments, the interaction model provides slightly better performance, but it is not significant. We still recommend users to use the linear model for better intepretbility.

4.2.3 Run LmTag to select tagSNPs

## testing with k = 200
LmTag tag --ld_model chr10_EAS_ld_fitted_model.txt \
      --eff chr10_EAS_CADD.txt \
      --vip VIP_GWAS_CLINVAR_ALL.txt \
      -k 200 \
      -o chr10_EAS_tagSNP.txt

Input argument:

Name	Description
--ld_model	fitted model ld file, generated by it_imputation_model.R
--eff	file provide infomation of effect score of input SNP
--exclude	list of SNPs that will be try to avoid to select by the algorithm
--vip	list of SNPs that will be try to prioritize to select by the algorithm
-k	k value of the beam search algorithm
-o	output file name

5. Output

LmTag output file is chr10_EAS_tagSNP.txt with following infomation

Name	Description
chr	chromosome of tag SNP
pos	position of tag SNP
id	typically isrsID of tag SNP - but depends on input ld file
sum_score	sum of impuation score - used for weighting in tag SNP selection
degree	degree of tag SNP in the graph
effect_score	effect score of tag SNP
flag	source of tag SNP - it can be normal, vip (from vip list), excluded (from excluded list)
tagged_pos	positions of tagged SNPs

6. Evaluation imputation accuracy performance

cat chr10_EAS_tagSNP.txt | grep -v "chr" | awk '//{printf "%s\t%s\n", $1, $2}'  > chr10_EAS_tagSNP_cleaned.txt


imputation_with_prebuilt_ref.sh -t chr10_EAS_tagSNP_cleaned.txt -r chr10_EAS_hg38_high_cov -o LmTag_chr10_EAS -p 16

compute_imputation_accuracy.R imputation=LmTag_chr10_EAS out=LmTag_chr10_EAS.Rdata

7. License

The Software is restricted to non-commercial research purposes.

8. Reference

Dat Thanh Nguyen, Quan Hoang Nguyen, Nguyen Thuy Duong, Nam S Vo, LmTag: functional-enrichment and imputation-aware tag SNP selection for population-specific genotyping arrays, Briefings in Bioinformatics, 2022;, bbac252, https://doi.org/10.1093/bib/bbac252

lmtag's Issues

Issue with compute_imputation_accuracy.R

Hello,

I encountered difficulties while attempting to replicate the example provided in the README file. Specifically, when executing the following command:

compute_imputation_accuracy.R imputation=naive_chr10_EAS out=naive_chr10_EAS.Rdata

I received the following error message:

Error in file(file, "rt") : cannot open the connection
Calls: read.delim -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'imputed_HG00428.txt': No such file or directory
Execution halted 

Environment

• R version 3.5.3 (2019-03-11) -- "Great Truth"
• PLINK v1.90b6.16 64-bit (17 Feb 2020)
• bcftools 1.19

Reproducibility Steps

I just followed the steps in the readme with the provided files. I also downloaded the model from the given link.

Thank you for your attention to this matter.