Extract subset of samples from multigenome vcf file

Question

[MAPK]

I have a multigenome vcf file. Suppose the file has samples A to Z, but I want to extract the subset of samples B to G and extract a small vcf file. How can I make such subset vcf file?

[GenoMax]

@Jorge Amigo's answer in this thread would be recent: How To Split Multiple Samples In Vcf File Generated By Gatk?

[MAPK]

@genomax2 Thanks, but this only explains how to extract individual sample per file. Is there a way to input the list of samples I want to extract (for example, samples B,C,D,E,F and G) and get a subset file with these samples only?

[stolarek.ir]

I don't know how to do it in vcf format, but you can convert into plink format (plink --double-id --vcf your.vcf --recode --make-bed --out your_output), then from generated fam file select the individuals you want and extract them with(plink --bfile your_plink --keep list_of_individuals --recode --out your_output). Then you can convert back to vcf if you wish :x

Answer 1

[Jorge Amigo]

from https://samtools.github.io/bcftools/bcftools.html#view

bcftools view -s samplelist

or

bcftools view -S samplefile

would do the job. docs are your friends ;)

Answer 2

[MAPK]

I have created this bash loop to loop over files (by chromosome or any vcf file). Then using vcf-subset tool, I was able to extract the subset file. Here, sample.txt is the list of samples per line. No need to tabix or bgzip parent vcf files with this method, but is a bit slower.

for i in /path/dir/*.vcf; do
    vcf-subset -c sample.txt "$i" | bgzip  -c > /get/inthis/dir/output_"${i##*/}"_.vcf.gz
done

[Jorge Amigo]

bcftools is faster than vcftools

for file in /path/dir/*.vcf; do
    bcftools view -Oz -S sample.txt $file > /get/inthis/dir/output_"${i##*/}"_.vcf.gz
done

[MAPK]

Although it is 10 times faster, the "problem" with bcftools is that it needs the variants VCF file to be bgzip compressed and tabix indexed. before using the code above you should do the following:

bgzip ALLsamples.vcf
tabix -p vcf ALLsamples.vcf.gz

[Jorge Amigo]

true, although it shouldn't be a problem

for file in /path/dir/*.vcf; do
    bgzip $file; tabix -p vcf $file.gz
    bcftools view -Oz -S sample.txt $file.gz > /get/inthis/dir/output_"${i##*/}"_.vcf.gz
done

Answer 3

[Pierre Lindenbaum]

GATK selectVariants https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_SelectVariants.php and option

--exclude_sample_file (file)

or

--sample_file (file)

[MAPK]

What would be the equivalent option in current GATK(4.1.2 or latest)? Is it --sample-name to extract samples from the wanted list?