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Old 04-17-2012, 02:50 AM   #1
a11msp
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Location: UK

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Default Calling genotypes on multiple trios

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!
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