Hi all - I'm stumped and need your help. I'm following the GATK best practices for calling variants with HaplotypeCaller in GVCF mode. One of my samples is NA12878, among 119 others samples in my cohort. For some reason GATK is missing a bunch of variants in this sample that I can clearly see in IGV but are not listed in the VCF. I discovered that the variant is being filtered out..reason being VQSRTranchesSNP99.00to99.90. The genotype is homozygous variant, DP is 243, Qual is 524742.54 and its known in dbSNP. I suspect this is happening to other variants.
How do I adjust VQSR or how tranches are used and variants get placed in? I supposed I need to fine tune my parameters...but I would think something as obvious as this variant would pass Filtering.