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GQ zero in reference mode and strand bias
Why do we get GQ = 0 at chr6:42946358 ?
Command used -
gatk-18.104.22.168/gatk HaplotypeCaller -I all_PE_sortedRG.bam -R hg19.fasta -L 6:42946053-42946662 -ERC BP_RESOLUTION -O temp_pe.vcf --dont-use-soft-clipped-bases true -new-qual true -bamout temp.bam
gvcf output at that position -
6 42946358 . T . . . GT:AD:DP:GQ:PL 0/0:191,45:236:0:0,0,5326
Its paired-end sequencing. Looking at IGV, all alt bases are around the end from one side of the strand. So, no actual variant call. Expectation is that GATK should be able to provide a confidence reference genotype.
bamout has no reads around that region.