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VCF to genotype file of specific format

I have a VCF per individual.

I'd like to take it, and convert it to the following format so that I have the alleles of the individual in the last two columns:

rsid chr pos ref alt

rs102 chr1 34 A G

Any package that does this already?

vcf awk bash genotypes
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updated by Shane McCarthy Shane McCarthy • written by David.shaw • David.shaw

3 answers

For REF and ALT in the last two columns:

bcftools query -f '%ID %CHROM %POS %REF %ALT\n' input.vcf

For the actual alleles of the individual in the last two columns:

bcftools query -f '%ID %CHROM %POS[ %TGT]\n' input.vcf | tr "/" " "
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written by Shane McCarthy Shane McCarthy

This doesn't quite work in regards to the actual alleles if some are phased and some aren't (because they are rare).

This worked:

bcftools query -f '%ID %CHROM %POS[ %TGT]\n' ../131.vcf | tr "|" " " | tr "/" " " | less -S

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written by David.shaw • David.shaw

Then replace the tr command at the end with

tr "/|" " "
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written by Shane McCarthy Shane McCarthy 
awk '! /\#/' file.vcf | awk -F '\t' '{print $3"\t"$1"\t"$2"\t"$4"\t"$5}'
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written by Vivek Vivek

No, This doesn't handle more than biallelic SNPs.

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written by David.shaw • David.shaw

GATK VariantsToTable https://www.broadinstitute.org/gatk/blog?id=7089

or my tool BioAlcidae see Taking genotypes out of a vcf file

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written by Pierre Lindenbaum Pierre Lindenbaum

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