Aligner/SNP caller for Illumina data

[sklages]

Hi,

to keep the number of false-positive-SNP-calls and thus the number of follow-up experiments (e.g. sanger control sequencing) as low as possible, I was wondering which software performs best on this task.

Fungi, human (enriched) datasets.

What are the experiences?

I surely will try a few, including Illumina's CASAVA, but some hints are welcome ..

Thanks,
Sven

[Jose Blanca]

We had exactly the same problem, but with plant transcriptomes. To solve it we developed a software named ngs_backbone. Even if you do not use this software you could take a look at the filters that we applied to look for the more promising SNPs.
Regards,

Jose Blanca

[sklages]

Thanks, Jose, I will surely have a look at 'ngs_backbone' and the filters used.

Sven