whatsHap didn't phase all variants

Question

[s2004341]

Hi there, I am using whatsHap to phase my filtered variants. The job was ran well and the output file generates normally. But when I was checking the contents of file, I found only a small proportion of SNPs has been phased. Anybody know why whatsHap didn't phase all SNPs, or is there some mechanism make this limit?

This screenshot was produced through "diff \ -biw \ bcftools_QUAL78_sample_1.vcf \ Phased_Q78_Horti_sample_1.vcf" which represents the phases part ("/" replaced by "|")

While other SNPs were still unphased.

Many thanks, Zitian

[4galaxy77]

WhatsHap can only phase variants if they are covered by reads which overlap with a different variant. So my guess is that the unphased variants didn't;t have that.

[s2004341]

Thank you, I'll check that!

[WouterDeCoster]

Your screenshot is rather unclear (hint: don't post screenshots but just paste the text and format it nicely with the 101010 button), but perhaps it is worth mentioning that phasing doesn't make a lot of sense for all these homozygous variants. You need heterozygous variants. In addition, I see most (if not all?) positions have a PS field in their genotype, and hence, are actually in a phase block.

Answer 1

[bouchenak.chuxi]

This may result from two possibilities :

1 - your have homozygotes genotypes ; thus no ''need" for phasing in this case.

2 - you used ''filtred variant" ; that causes the tool to run wrongly and have poor data. it would be best to phase the original vcf containing all the variants, then filtering it