Snp Calling Tools And Costs

Question

[Andrea_Bio]

Hello

Please can you tell me what are the main software tools people in the industry use for snp calling and to obtain whole genome SNP sets? I can look up lots of different algorithms for snp calling but i don't know what the real people in sequence labs actually use

I'd also like to know what output format they produce and how much they cost to produce a whole genome snp set.

thanks

Answer 1

[Ian]

In terms of SNP calling:

COBALT (Illumina orientated). I haven't used this as I am SOLiD based.

ComB (works in conjunction with the PerM aligner (both SOLiD based). However, ComB only finds SNPs as PerM does not allow gapped alignments.

But to be honest my SNP calling projects so far have used the samtools protocols, in conjunction with BFAST. This also allows short INDELs to be discovered.

IMPORTANT NOTE: In my experience (and also the general feeling i think) is that local realignment of mapped reads is essential, for example SRMA, which I have used successfully. Otherwise INDELs create spurious SNP calls!!!

Answer 2

[brentp]

The SNP (variant) caller in samtools has a very good use and explanation.

Also the GATK tool seems very popular.

Answer 3

[User 59]

Why don't you have a look at what the people who handle a 1000 genomes or more use? The supplementary materials to their Nature paper. There's also this previous BioStar thread.