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Open Source Compliant Diploid Variant Caller comparable to GATK Haplotype Caller?

Is there a Diploid Variant Caller comparable algorithmically and in performance to GATK 2.x or 3.x Haplotype Caller but with an Open Source Compliant license (non-restrictive use)?

gatk variant calling
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updated by Ram Ram • written by 14134125465346445 14134125465346445

4 answers

This is always worth a read (from Brad Chapman).

tl;dr?

FreeBayes is pretty good. (MIT licenced)

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updated by Ram Ram • written by User 59 User 59

Thanks Brad, these posts are a great resource.

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written by User 59 User 59

From what I know, you can also use ISAAC aligner + variant caller which is developed by illumina, playtpus from Welcome Trust is another possible candidate. From my group's experience, ISAAC is more stringent whereas platypus' stringency is somewhere between GATK HC and ISAAC

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updated by Ram Ram • written by Sam Sam

Platypus is developed by Oxford, not sanger.

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written by lh3 lh3

Well, it is from the Wellcome Trust Centre for Human Genetics in Oxford if we are to be really precise. I think that makes you both correct.

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updated by Ram Ram • written by User 59 User 59

Good news, hopefully, for anyone reading this thread: GATK is returning to a fully open-source license (BSD 3-clause). For more details, see the press release from Broad and my post on the GATK blog.

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written by vdauwera vdauwera

Depends on what you define as 'comparable'.

http://varscan.sourceforge.net/

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updated by Ram Ram • written by Coryza Coryza

Performance would be easy, functionality and quality I guess is the difficult part.

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written by William William

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