Hi!
I used Debreak to compare my assembly to a reference genome which is haploid. And I am confused by the genotype information in the Vcf file. For example, This duplication is detected as multi-allelic yet the genotype is 1/1. Why wasn't it reported as 1/2?
NC_031467.1 1047294 DB2 N . PASS END=1047439;CHR2=NC_031467.1;SVLEN=146;SUPPREAD=41;MAPQ=60;SVMETHOD=DeBreak;SVTYPE=DUP;MULTI GT 1/1
Hi!
I used Debreak to compare my assembly to a reference genome which is haploid. And I am confused by the genotype information in the Vcf file. For example, This duplication is detected as multi-allelic yet the genotype is 1/1. Why wasn't it reported as 1/2?
NC_031467.1 1047294 DB2 N . PASS END=1047439;CHR2=NC_031467.1;SVLEN=146;SUPPREAD=41;MAPQ=60;SVMETHOD=DeBreak;SVTYPE=DUP;MULTI GT 1/1