Variation Callers?

[oiiio]

I am analyzing some whole genome data and at the moment I use GATK for indels and SNPs. What are some other tools or pipelines out there for whole genome analysis?

For example I read the HugeSeq paper, and I saw pindel, CNVnator, BreakDancer, and BreakSeq. Does anyone have other recommendations or preferences among these ?

And do you (or how do you ) combine results from two programs, such as UnifiedGenotyper and Pindel?

[Jane M]

Hello,

There is the same topic here: http://seqanswers.com/forums/showthread.php?t=15000, in case it helps.

There are also SomaticSniper, MuTect & SNVMix (only for SNPs) and VarScan...
I have not yet any experience in combining results from two programs, so I cannot help, but I am interested in the answer

[Zam]

one more for the long list:

http://seqanswers.com/forums/showthread.php?t=16695

[aeonsim]

Real time genomics (rtg) commercial great for trios
Freebayes
Samtools

Are other good tools.

[oiiio]

Thanks for the replies so far,

I'm extremely interested in the combinations of tools - like HugeSeq's pindel and unified genotyper combo - that people think form really comprehensive analysis?

[dnusol]

Hi there

it seems that FreeBayes has not been published yet. Is this so?

http://arxiv.org/abs/1207.3907

Thanks

Dave

[girlmonkey]

We are using Platypus (http://www.well.ox.ac.uk/platypus) for our Haloplex panels.