htslib.org/workflow - legacy gatk commands

[keiranmraine]

Hi,

Sorry if this isn't the correct place to raise.

The v4+ versions of gatk are quite different and specifically do not have the jar file (GenomeAnalaysisTK.jar) indicated in the above document. A secondary change is that the commands are called through a wrapper.

This has caused confusion to some of our users when they attempt to follow this guide, especially as the legacy jar files and gatk documentation are hard to track down.

Regards,
Keiran

[dpryan79]

You're looking for the GATK forum: https://gatkforums.broadinstitute.org/gatk/

[jmarshall]

I think Keiran is looking for samtools/www.htslib.org — which in fact he has filed issues on in the past 😄

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