SNP calling software in pooled samples

mrxcm3 · 11-03-2010, 10:25 AM

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

lh3 · 11-03-2010, 11:49 AM

http://genome.cshlp.org/content/earl...7.110.abstract

krobison · 11-03-2010, 12:08 PM

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.

Jose Blanca · 11-03-2010, 10:38 PM

The exactly same topic has been discussed in the samtools list a couple of days ago.

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11-03-2010, 10:25 AM	#1
mrxcm3 Junior Member Location: Nottingham Join Date: Oct 2010 Posts: 9	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

11-03-2010, 11:49 AM	#2
lh3 Senior Member Location: Boston Join Date: Feb 2008 Posts: 693	http://genome.cshlp.org/content/earl...7.110.abstract

11-03-2010, 12:08 PM	#3
krobison Senior Member Location: Boston area Join Date: Nov 2007 Posts: 747	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.

11-03-2010, 10:38 PM	#4
Jose Blanca Member Location: Valencia, Spain Join Date: Aug 2009 Posts: 70	The exactly same topic has been discussed in the samtools list a couple of days ago.