VEP generated VCF file filtering using gnamAD, CADD , dbNSF etc with out loosing sample specific variants.

Question

[Nai]

I have vcf annotated by VEP. I would like to filter this file on the basis on gnomAD, CADD and revel. When I am doing this via bcftools then I lost samples from vcf file. I request for help to filter in quick manner. I tried in dplyr but it failed due to missing column header information like gnomAD, CADD.

[Pierre Lindenbaum]

"When I am doing this via bcftools then"

Answer 1

[Nai]

bcftools +split-vep -c gnomAD_AF:Float all_merged_VEP_annotated_ensembl.vcf -i 'gnomADg_AF<=0.001' -Ov -o global.vcf

In this file there was sample specific variants.

bcftools +split-vep -f '%CHROM\t%POS\t%REF\t%ALT\t%CSQ\n' -d -A tab input.vcf Then outfile does not have sample columns. even i mentioned %CSQ\t%Sample1\t%Sample2...\n'