@isaacovercast@dereneaton I found one problem in the vcf file: some allele value in GT is 3, e.g. 0/3, which indicate the third allele list in ALT. However, there are only two allele list in ALT. Do you guys know the reason? Thanks a lot !
1834 41 . T G,A 13 PASS NS=17;DP=890 GT:DP:CATG 0/3:29:6,0,23,0