Question: Open Source Compliant Diploid Variant Caller comparable to GATK Haplotype Caller?
3
gravatar for 14134125465346445
5.2 years ago by
United Kingdom
141341254653464453.5k wrote:

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 • 3.0k views
ADD COMMENTlink modified 2.6 years ago by vdauwera960 • written 5.2 years ago by 141341254653464453.5k
6
gravatar for Daniel Swan
5.2 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

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

http://bcbio.wordpress.com/2013/10/21/updated-comparison-of-variant-detection-methods-ensemble-freebayes-and-minimal-bam-preparation-pipelines/

tl;dr?

FreeBayes is pretty good: https://github.com/ekg/freebayes (MIT licenced)

ADD COMMENTlink modified 5.2 years ago • written 5.2 years ago by Daniel Swan13k
5

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/

ADD REPLYlink written 5.2 years ago by Brad Chapman9.5k
2

Thanks Brad, these posts are a great resource.

ADD REPLYlink modified 5.2 years ago • written 5.2 years ago by Daniel Swan13k
3
gravatar for Sam
5.2 years ago by
Sam2.5k
New York
Sam2.5k wrote:

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

ADD COMMENTlink modified 8 weeks ago by RamRS25k • written 5.2 years ago by Sam2.5k

Platypus is developed by Oxford, not sanger.

ADD REPLYlink written 5.2 years ago by lh331k

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.

ADD REPLYlink written 5.2 years ago by Daniel Swan13k
2
gravatar for vdauwera
2.6 years ago by
vdauwera960
Cambridge, MA
vdauwera960 wrote:

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.

ADD COMMENTlink written 2.6 years ago by vdauwera960
0
gravatar for Coryza
5.2 years ago by
Coryza380
Netherlands
Coryza380 wrote:

Depends on what you define as 'comparable'.

http://varscan.sourceforge.net/

ADD COMMENTlink modified 8 weeks ago by RamRS25k • written 5.2 years ago by Coryza380

algorithmically or in performance

ADD REPLYlink written 5.2 years ago by 141341254653464453.5k

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

ADD REPLYlink written 5.2 years ago by William4.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1978 users visited in the last hour