What are the SNP calling programs?

[foxyg]

Hi guys,

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

Thanks

[krobison]

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

Other tools can be found here.

[Jose Blanca]

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.