jjuhyunkim
commented
1 year ago - element support HG002 : A / G HG003 : A / G HG004 : G / G The bold character indicates the expected inherited haplotype.
The variant calling result was correct
The variant is called heterozygous in hg002, and the variant appears as hetero in paternal and homozygous alt in maternal. However, mat hifisam hap1 does not have the alternative variant, and this haplotype was used in the hg002 diploid reference. Therefore, the variants in chr16_maternal should have the G alt allele at the loci not only in mat hap1 but also in the hg002 maternal haplotype.
Assembly Region
chr16_MATERNAL:26017038-26017038
Assembly Version
v0.7
DeepVariant Call
chr16_MATERNAL 26017038 chr16_MATERNAL_26017038_A_G A G 60 . AF=0.666667;AQ=60 GT:AD:DP:GQ:PL 0/1:10,8:18:60:60,0,82 0/1:13,5:18:47:47,0,67 1/1:0,12:12:33:55,33,0