I'm trying to phase a human sample and I'm getting the following separation of reads in the two haplotypes:
Haplotype 1 (the bottom one) looks great with the big insertion (~160 bp) and variants and all. But haplotype 2 (the top one) doesn't seem as consistent with all the different insertions, there are only a couple variants shared between all the reads. Is this a normal phasing result? Also there are A LOT of variants in haplotype 1 and not all that much in haplotype 2.
The phasing was done using three variants, I don't have much depth in this run, so I was only able to find this regions with variants with enough depth for haplotyping.