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Variant Calling with .NET Bio

Jan 16, 2013 at 3:45 PM

I think it would be great to have an ability to call variants in resequencing efforts using .NET Bio.  That is have the capability to do phase 1 and phase 2 analysis steps outlined here:

http://www.broadinstitute.org/gatk/guide/topic?name=best-practices

There are two main requirements for this:

1-Align reads to reference genome.

2-Call variants in this alignment.

My understanding right now is that neither 1 nor 2 is currently available in .NET Bio, though things very close to 1 are.

For calling variants, dong mentioned the SAMTOOLs (by which I think he meant the bcftools package), and the GATK.  I am more familar with the GATK (and am slightly under the impression it outperforms bcftools) and so was going to start looking in to how their code works for calling SNPs, but am open to any other ideas, thoughts, suggestions.  What do people think? 

 

Feb 6, 2013 at 2:00 PM
Nigel - aligning reads to the ref genome is a pretty high priority use case. I take it you want the solution to remain within the managed code world? don't know enough about the structure of snap to know whether a short read alignments can be handled by managed code, but one would have thought so. So maybe that code base might have something to offer? Anyone got any thoughts?