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Old 11-03-2010, 10:25 AM   #1
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Default SNP calling software in pooled samples

I have some very deep seq data for a small genomic region (50kb) - generated in pooled samples using SOLiD - and I am looking to discover rare variants.

Can anyone recommend any good SNP callers for pooled data? So far I have tried GATK (which is not suitable), VarScan, Syzygy and standard pileup (samtools). Anyone able to suggest other I should check out? Thanks
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Old 11-03-2010, 11:49 AM   #2
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Old 11-03-2010, 12:08 PM   #3
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The list in the software wiki is always growing (category: SNP discovery. It might be worth having a second category for ones which work on pools -- I'm sure there are some you haven't listed (though I have not tried any of them).

It looks like SNPSeeker and CRISP definitely fall in that categoryl; I think QCALL is not in this space but I could easily be wrong.
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Old 11-03-2010, 10:38 PM   #4
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The exactly same topic has been discussed in the samtools list a couple of days ago.
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