Calling Genotypes On Multiple Trios
1
1
Entering edit mode
12.2 years ago
a11msp ▴ 120

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 snp next-gen samtools gatk • 3.0k views
ADD COMMENT
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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 REPLY
3
Entering edit mode
12.2 years ago
Bioinfosm ▴ 620

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

ADD COMMENT
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 2771 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6