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g.vcf GQ of HOMREF block
I was looking at one of our g.vcf files, and I noticed the following homref block at the beginning of the file.
END=195186 GT:DP:GQ:MIN_DP:PL 0:70:99:3:0,117
If I interpret this correctly, the block goes from position 1 to 195186, has an average depth of 70, and a GQ of 99, which is the maximum value.
However, the MIN_DP (lowest DP in the homref block) shows a read depth of 3. Should a read depth of 3 not get a lower QC score, in which case the homref block should have been split up in multiple parts, according to the differing GQ's.
I want to know because I am thinking of using .g.vcf files to generate fasta files to use in phylogenetic analysis, since that would allow me to also include the conserved parts of the genome in the analysis. However, if areas with read depth of 70 and 3 are in the same homref block, it becomes difficult to do any meaningful filtering on things like read depth.