Closed rhshah closed 5 years ago
Try GATK 4
If you need it, this is the Dockerfile we use with Conpair which contains GATK 3.8: https://github.com/mskcc/vaporware/blob/master/containers/conpair/Dockerfile
I will add the older version with 3.3.0 anyway so you can have it ready, but GATK 4 is easily available in https://hub.docker.com/r/broadinstitute/gatk/tags?page=1.
I have made the container for 3.3.0, located here https://hub.docker.com/r/mskcc/gatk
Also it's in feature/gatk_3.3.0
branch
I am assuming its safe to use the GATK4 image
directly from GATK official Docker-Hub repo rather than building our own GATK image using a dockerfile. Correct?
The module for BQSR has been renamed to ApplyBQSR
in GATK4 and all the parameters have been renamed as well.
I think we should discuss these in the planning meeting before we change anything, from what you are describing @shalabhsuman looks like lot has changed, if that is the case lets build right now things for GATK 3.3.0 with PrintReads
continuing with GATK4..Moving this to #32
Tool: GATK3 PrintReads Location: https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.3-0-g37228af Version: 3.3.0