Hello, As I understand, QUAL is a representation of accuracy of genotyping. But what does a '.' represent under the QUAL column in a VCF file? I do not have any numeric value for Phred-scaled score for assertion of ALT allele in the entire column.
What does this mean for filtering low quality SNPs or genotypes?
EDIT: More information:
As I was looking as a filtered.recoded VCF file, I went back & checked the raw VCF file as well. This file had all the values for QUAL & INFO field. My service provider have responsed as 'The TASSEL-GBS pipeline does not calculate quality scores for any sites, but assigns an arbitrary, uniform value of 20 for each SNP in the VCF files. In my VCF files, and in all four cases there is only 1 QUAL score (20) for all SNPs which somehow appears a a '.' in the filtered recoded file. So, I should not use minQ for filtering SNPs, right?