Question: Require Genotypes In Vcf File In Order To Output Frequency Statistics
gravatar for ja4123
10 months ago by
ja41230 wrote:

I have a merged .vcf file, that although wasn't merged using vcftools seems almost identical to vcf-merge files. If I try and use --freq to calculate allele frequencies from this file I get the error message "Require Genotypes in VCF file in order to output Frequency Statistics". This seems odd as the file has the same GT:GQ:PL format as other .vcf files.

I was wondering if anyone knows what vcftools uses to calculate --freq and why I am getting this error message. I have gone back to source files, merged these in vcftools then performed --freq with this file, this time the analysis "works" but I get incorrect allele frequencies (compared to working them out by hand).


ADD COMMENTlink modified 10 months ago • written 10 months ago by ja41230

Can you grep the CHROM... header line and the first couple lines of the VCF file and paste it here? IE the output from: grep -m 1 "^#CHROM" file.vcf and grep -m 5 -v "^#" file.vcf

ADD REPLYlink modified 10 months ago • written 10 months ago by David Minkley10
gravatar for David Minkley
10 months ago by
University of Victoria
David Minkley10 wrote:

Is the header information for the VCF file correct? If the GT entry is missing in the header then vcftools may assume it's also absent from the body of the file.

ADD COMMENTlink written 10 months ago by David Minkley10
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