Trim gnomAD v3.1.2

Hello!

I'm wondering if anyone has written code, or knows of BCFTools/VCFTools/other published tool, to trim gnomAD v3.1.2 down from its current monstrosity (~3Tb for the all chromosomes) into a smaller utility for purposes of variant filtering in rare disease variant annotation.

Essentially I want to only keep a handful of annotations to slim this down, focusing on:

n_hom_alt_global
AF_global
AC_global

The ideal solution would let me specify which annotations to keep (maybe as a list), and which to remove.

Figured I'd ask before writing something myself.

Thanks! Phil

parser genomics gnomad vcf

• 1,738 views • link

updated 3.3 years ago by Ram

• written 3.3 years ago by Phillip •

What about a simple bcftools query? Unfortunately, you'll need a workaround to manage fields. For INFO fields, a simple -f <(cat fields.list | tr "\n" "\t") might work. This could be another option, although I've never tried it: https://vcf-kit.readthedocs.io/en/latest/vcf2tsv/

• 0 views • link

written 3.3 years ago by Ram

1 answer

using bcftools annotate

 wget -O - "https://storage.googleapis.com/gcp-public-data--gnomad/release/3.1.2/vcf/genomes/gnomad.genomes.v3.1.2.sites.chr22.vcf.bgz" |\
bcftools annotate -x '^INFO/nhomalt_popmax,INFO/AF,INFO/AC,FILTER,ID,'

(...)
chr22   10518128    .   G   A   .   .   AC=0;AF=0
chr22   10518128    .   G   T   .   .   AC=0;AF=0
chr22   10518144    .   A   G   .   .   AC=0;AF=0
chr22   10518147    .   G   T   .   .   AC=0;AF=0
chr22   10518152    .   G   T   .   .   AC=1;AF=4.8216e-05;nhomalt_popmax=0
chr22   10518153    .   G   C   .   .   AC=1;AF=4.85484e-05;nhomalt_popmax=0
chr22   10518174    .   G   A   .   .   AC=0;AF=0
chr22   10518183    .   G   A   .   .   AC=3;AF=0.000185117;nhomalt_popmax=1
chr22   10518211    .   G   A   .   .   AC=1;AF=6.71231e-05;nhomalt_popmax=0
chr22   10518213    .   G   A   .   .   AC=0;AF=0
chr22   10518213    .   G   GA  .   .   AC=37;AF=0.00246831;nhomalt_popmax=12
chr22   10518213    .   GA  G   .   .   AC=4;AF=0.00026688;nhomalt_popmax=0
chr22   10518250    .   G   A   .   .   AC=2;AF=0.000121551;nhomalt_popmax=1
chr22   10518251    .   C   T   .   .   AC=11;AF=0.000672125;nhomalt_popmax=5
chr22   10518275    .   T   A   .   .   AC=0;AF=0
chr22   10518278    .   G   A   .   .   AC=1;AF=5.97514e-05;nhomalt_popmax=0
chr22   10518282    .   A   G   .   .   AC=2;AF=0.000118301;nhomalt_popmax=1

• 0 views • link

written 3.3 years ago by Pierre Lindenbaum

bcftools annotate takes a -C file input that might be useful here.

• 0 views • link

written 3.3 years ago by Ram