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Variants found in GVCF but not in VCF
Suppose the main difference between GVCF and VCF is the non-variant record.
Curiously, I found some variants were called in GVCF but not in VCF.
This is the variant I found in GVCF but couldn't found in VCF:
19 55665584 . A C,<NON_REF> 10.01 . DP=4;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQ=14400.00 GT:AD:DP:GQ:PL:SB 1/1:0,2,0:2:6:36,6,0,36,6,36:0,0,2,0
Although I can filter it out by its low DP but I still want to know why it happened.
Is there some different calling step or algorithm in HaplotypeCaller between calling GVCF and VCF that make this difference?