I'm trying to extract allele frequency information for all variants in the latest ExAC data release. I'm currently using vcftools version 0.1.13, and am coming into errors that relate, I think, to versions.
When I validate the ExAC data VCF file, I get an error message for every INFO line in the file, that says something like the below:
>> vcf-validator ExAC.r0.3.1.sites.vep.vcf INFO field at 1:13404 .. INFO tag [AC_Het=0,1,0] expected different number of values (expected 2, found 3) FILTER field at 1:13418 .. The filter(s) [AC_Adj0_Filter] not listed in the header.
This suggests, I believe, that the ExAC data VCF file is not in the format vcftools wants it to be, which is v4.0, v4.1 or v4.2. If this is true, how do I make the ExAC data VCF file vcftools- compatible?
The real error I'm trying to overcome comes from when I try to extract the frequency information:
>> vcftools --gzvcf ExAC.r0.3.1.sites.vep.vcf.gz --freq --chr 1 --out chr1_freq VCFtools - v0.1.13 (C) Adam Auton and Anthony Marcketta 2009 Parameters as interpreted: --gzvcf ExAC.r0.3.1.sites.vep.vcf.gz --chr 1 --freq --out chr1_freq Using zlib version: 1.2.8 After filtering, kept 0 out of 0 Individuals Error: Require Genotypes in VCF file in order to output Frequency Statistics.
Can anyone help me out?