Hi,
some picard tools like MergeSamFiles were ported to GATK 4 beta. Now in the release version they are described as picard tools again. Even though they are part of the GATK and can be used as such.
see here:
https://software.broadinstitute.org/gatk/documentation/tooldocs/current/picard_sam_MergeSamFiles.php
https://software.broadinstitute.org/gatk/documentation/tooldocs/4.beta.5/org_broadinstitute_hellbender_tools_picard_sam_MergeSamFiles.php
Which one should I use? Will there be documentation for the GATK versions?
Thanks and best regards,
Daniel