Avilable better SNPcalling tools (except GATK and Samtools)

Question

[murali]

Hi,

I am beginner in the field of NGS. I want to do SNPcalling and using GATK as well as Samtools, but currently GATK not supporting latest version of hg38. I am using the Illumina seq data and Iontorrent PGM datasets. Can you suggest better tools for SNPcalling other than GATK and Samtools ?

I read earlier posts Genotype And Snp Calling Review Papers and Snp Calling Tools And Costs.

It could be really nice, if you can provide your review and feed back or opinion as well as scientific citations about your used tools for SNPcalling?

[Ram]

hg38 is not mature yet, most analyses I've seen are on hg19/GRCh37. You might wanna use that for now. hg38 still needs quite a bit of annotation work and/or liftover before it becomes mainstream.

Answer 1

[lh3]

Both freebayes and platypus are very good. In terms of algorithms, they are better than samtools.