Use bcftools to find carriers of variants
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2.3 years ago

I would think this is a frequent task, but it seems I cannot find a bcftools-approach to tackle this: when looking at large VCF files with (rare) variants, I often want to figure out the sample identifier of the carrier(s). I think one solution could be to add a field to the INFO field "CARRIERS=<list>", or alternatively make a tsv export of the VCF.

I now do this in python with cyvcf2, works great, but it feels like an unnecessary wrapper.

Any bcftools wizards? :)

vcf bcftools • 1.3k views
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3
Entering edit mode
2.3 years ago

bcftools query should help here, e.g.:

bcftools query -i'GT="het"' -f '%CHROM  %POS  [%SAMPLE ]\n' variants.bcf
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1
Entering edit mode
2.3 years ago

using vcffilterjdk ( http://lindenb.github.io/jvarkit/VcfFilterJdk.html à , the following cmd will add the INFO/SAMPLES containing the name of the HET or HOM_VAR samples.

bcftools view input.vcf.gz |\
awk '/^#CHROM/ {printf("##INFO=<ID=SAMPLES,Number=.,Type=String>\n");} {print;}' |\
java -jar dist/vcffilterjdk.jar -e 'final List<String> L= variant.getGenotypes().stream().filter(G->G.isHet() || G.isHomVar()).map(G->G.getSampleName()).collect(Collectors.toList()); return new VariantContextBuilder(variant).attribute("SAMPLES",L).make();'
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