SNP calling software in pooled samples

[mrxcm3]

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]

http://genome.cshlp.org/content/early/2010/11/01/gr.109157.110.abstract

[krobison]

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]

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