whatsHap didn't phase all variants
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15 months ago
s2004341 • 0

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?

enter image description here

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

whatsHap phasing • 742 views
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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.

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Thank you, I'll check that!

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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.

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3 months ago

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

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