Im trying to filter a vcf file I've got from genomAD (Exome VCF files) for MAF > 0.01, using vcftools but I get an error I cant figure out why.
I use this command:
vcftools --vcf gnomad.exomes.r2.0.2.sites.vcf --recode --maf 0.01 --out gnomad.exomes.r2.0.2.sites.filtered.MAF01.vcf
but I get the following error "" VCFtools - UNKNOWN (C) Adam Auton and Anthony Marcketta 2009
Parameters as interpreted: --vcf gnomad.exomes.r2.0.2.sites.vcf --maf 0.01 --out gnomad.exomes.r2.0.2.sites.filtered.MAF01.vcf --recode
After filtering, kept 0 out of 0 Individuals Outputting VCF file... Error: Require Genotypes in variant file to filter by frequency and/or call rate
"" I tried to check with HTSLIB if its identified as vcf file and yes!
$ htsfile gnomad.exomes.r2.0.2.sites.vcf
gnomad.exomes.r2.0.2.sites.vcf: VCF version 4.2 variant calling text
I tried with the bgzipped version of the file which I directly get from genomAD using --gzvcf tag in vcftools, but still the same problem...
There is a similar questoin from more than a year ago without any answers: vcftools flags --mac and --max-mac giving an empty output file
It would be great if someone gives me any clue of what can be the problem!