Upgrade samtools in the GATK docker image to 1.10 (at least)

[LeeTL1220]

trafficstars

Feature request

Tool(s) or class(es) involved

The docker image would need to be updated (gatkbase docker image). See line ~17 in scripts/docker/gatkbase/Dockerfile

Description

Can you include a later version of samtools in the GATK image? The current samtools version (1.7) does not support crams. I believe that you would need to update gatkbase to make this change.

Additional suggestion, which should not be a requirement for closing this issue: you may want to fix the versions of the software in gatkbase (lines ~6-25 in scripts/docker/gatkbase/Dockerfile).

Note: I have only replicated this issue in us.gcr.io/broad-gatk/gatk:4.2.6.1

[droazen]

Assigning to @lbergelson