Question: Calling Genotypes On Multiple Trios
1
gravatar for a11msp
7.6 years ago by
a11msp110
European Union
a11msp110 wrote:

Hi everyone,

I have a set of eight Illumina-sequenced trios for an organism, for which a reference genome is available. I'd now like to call genotypes on these data taking advantage of both a "classic" multisample and trio-aware approaches. I understand that bcftools (part of samtools suite) can do trio-aware calling, but I'm not sure it can work with multiple trios. At the same time, GATK (and samtools too?) can run a Bayesian model based on observed allele frequencies assuming a flat population structure.

So my question is - are there any tools that can combine both approaches?

Thanks a lot!

genetics next-gen samtools snp gatk • 2.0k views
ADD COMMENTlink written 7.6 years ago by a11msp110

You can always hard filter by taking the union of the parents intersected with the child. The child must contain only SNVs found in the parents.

ADD REPLYlink modified 7.6 years ago • written 7.6 years ago by Zev.Kronenberg11k

Thanks - I currently do something along these lines, but I was wondering if a more general way of taking this info into account when computing SNP quality scores was available...

ADD REPLYlink written 7.6 years ago by a11msp110

mpileup in samtools can leverage calling multiple individuals. I believe this is beneficial when there is evidence of a SNP, but low coverage. http://samtools.sourceforge.net/mpileup.shtml

ADD REPLYlink written 7.6 years ago by Zev.Kronenberg11k
3
gravatar for Bioinfosm
7.6 years ago by
Bioinfosm620
earth
Bioinfosm620 wrote:

VAAST is one tool, especially its upcoming p-VAAST version that can be of use for that analysis.

ADD COMMENTlink written 7.6 years ago by Bioinfosm620

Yes. p-VAAST is ideal for disease gene hunting in families. We are happy to hear that people are adopting VAAST.

ADD REPLYlink written 7.6 years ago by Zev.Kronenberg11k

Thanks, will try out VAAST! Could you let me know a bit more about the upcoming p-VAAST and when it's expected to appear (which would be very good to know for my project's logistics)

ADD REPLYlink written 7.6 years ago by a11msp110

from what I heard, its coming in May-Jun timeframe

ADD REPLYlink written 7.6 years ago by Bioinfosm620

It's close. We are testing it on some real datasets now.

ADD REPLYlink written 7.6 years ago by Zev.Kronenberg11k

Great, thanks! And what will be the key difference from the existing VAAST?

ADD REPLYlink written 7.6 years ago by a11msp110
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