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How to make 4-column annotation file

Hi everyone,

I've been following regenie to perform analyses. In its 2nd step a 4-column annotation file is needed. The format is

1:55039839:T:C PCSK9 LoF
1:55039842:G:A PCSK9 missense

According to snpEFF documentation, its output is in vcf format, which I think might be difficult to convert to this format. Therefore I would like to know which tool is suitable for generating such format.

Thank you.

snpeff regenie vep annotation
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updated by zx8754 zx8754 • written by Lloyd_641 • Lloyd_641

1 answer

something like:

bcftools query -f '%CHROM:%POS:%REF:\t%INFO/ANN\n' in.vcf  |\
awk -F '\t' '{N1=split($2,ann,/[,]/);for(i=1;i<=N1;i++) {split(ann[i],b,/[|]/);printf("%s%s %s %s\n",$1,b[1],b[4],b[2]);} }'
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks so much Pierre Lindenbaum ! However it concerns me that my vcf file is quite large (as it contains a huge number of samples) and it has taken hours just to perform the bcftools stats function. Are you familiar with any annotation tool that takes just variant IDs or that outputs in a form simpler than vcf?

Best regards

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updated by zx8754 zx8754 • written by Lloyd_641 • Lloyd_641

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