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Old 10-07-2010, 07:01 AM   #1
Location: US

Join Date: May 2010
Posts: 54
Default What are the SNP calling programs?

Hi guys,

What are the popular SNP calling programs out there. I tried samtools, and GATK, are there any other good ones out there?

foxyg is offline   Reply With Quote
Old 10-07-2010, 07:48 AM   #2
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Location: Boston area

Join Date: Nov 2007
Posts: 747

I've been using SNVMix, but haven't tried to benchmark it.

Other tools can be found here.
krobison is offline   Reply With Quote
Old 10-08-2010, 06:19 AM   #3
Jose Blanca
Location: Valencia, Spain

Join Date: Aug 2009
Posts: 70

We have an SNP caller deveped to call and filter highly reliable SNPs to be used in genotyping experiments. You can take a look at ngs_backbone.
We have experimentaly validated the result in a tomato experiment and we have obtained very good results.
Jose Blanca is offline   Reply With Quote

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