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

Question

[14134125465346445]

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)?

Answer 1

[User 59]

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

tl;dr?

FreeBayes is pretty good. (MIT licenced)

[Brad Chapman]

Thanks Daniel. We've been working on an update to this that includes samtools 1.x and Platypus as two other good choices:

http://bcbio.wordpress.com/2014/10/07/joint-calling/

[User 59]

Thanks Brad, these posts are a great resource.

Answer 2

[Sam]

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

[lh3]

Platypus is developed by Oxford, not sanger.

[User 59]

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.

Answer 3

[vdauwera]

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.

Answer 4

[Coryza]

Depends on what you define as 'comparable'.

http://varscan.sourceforge.net/

[14134125465346445]

algorithmically or in performance

[William]

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