I have a known variant that appears in the GVCF but is filtered out in the VCF in two different samples. They look ok to my naive eye - does anyone have any thoughts based on the GVCF calls below?
chr20 4699605 rs1799990 A G,<NON_REF> 177.64 . BaseQRankSum=-1.817;DB;DP=30;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=108000,30;ReadPosRankSum=1.009 GT:AD:DP:GQ:PL:SB 0/1:19,9,0:28:99:185,0,568,242,594,836:10,9,4,5
GATK version used: 126.96.36.199
Command used: nfcore/sarek haplotypecaller
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