How to make 4-column annotation file

Question

[Lloyd_641]

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.

Answer 1

[Pierre Lindenbaum]

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]);} }'

[Lloyd_641]

Thanks so much pierre.peterlongo ! 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

[Pierre Lindenbaum]

parallelize by regions

[Lloyd_641]

Thanks, I' check that