Can Bcftools And Vaast Call Phased Genotypes?

Question

[a11msp]

Hi everyone,

I'm aware that samtools can produce phased genotypes using the phase option. Since I'm using trio designs (as some of you may have seen from my previous post...), I used bcftools instead. I'm wondering if the resulting vcf contains phased genotypes and if not, what would be the best phasing protocol?

I'm also wondering, in light of the very helpful suggestion to my previous post to try out VAAST, whether this tool can call phased genotypes.

Many thanks!

[Raymond301]

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Answer 1

[Zev.Kronenberg]

VAAST is the Variant Annotation, Analysis and Search Tool. It can annotate variants but does not call them. The second part of the VAAST pipeline is the search tool. In the case of trio data you provide the child genotypes and the parents genotypes separately along with a background file (1000 genomes ect.). This has worked well for Miller syndrome and Ogden syndrome. These cases used trio and quartet family data.