hapcut2 output and figures

Question

[rob234king]

I have run Hapcut2 and have a VCF file. I can't see in the VCF where it has assigned the snp to one haplotype or the other, any ideas where that information is kept? I can see it in the other hapcut output file but not the VCF which seems wrong. I assume can separate the two haplotypes in vcf to two files so can have two tracks for each haplotype in a browser. Any prior experience of phased snp output would be welcome. Also any ideas how to produce a phased block chromosome image using the VCF or hapcut2 file. Assume someone must have done this before

Answer 1

[Peter Chung]

the allele column will change / to | which means phased