Ngs Tool Analysis For Snp&Indel Calling Of Pooling Data

Question

[marcodpc]

What are the best and most used analysis tool actually, for SNP and indel calling of pooled data?

I'm using GATK & Freebayes that have specified options for data in pool.

Now I have found CRISP.

Are there others and good tool that I ignore?

Thanks!

[Medhat]

i think that may help Which are the best collections of bioinformatics tools for NGS analysis and sequence files management?

Answer 1

[Zev.Kronenberg]

I have had good luck with SNVer. I haven't benchmarked it or compared it to other tools, but I have found several GWAS candidates with it. You might also be interested in PoPoolation.