Missing tasks will be added + strung together for three GATK Best Practice workflows. I have been using these a lot for various projects and think its makes sense they are housed here in the public domain. There will be slight variations (e.g. using Samblaster + Sambamba over MarkDuplicates) but will explain this in more detail elsewhere.
Broad does have WDL workflows for these but they are pretty messy if you ask me (see here) and are no longer maintained
Description
Missing tasks will be added + strung together for three GATK Best Practice workflows. I have been using these a lot for various projects and think its makes sense they are housed here in the public domain. There will be slight variations (e.g. using Samblaster + Sambamba over MarkDuplicates) but will explain this in more detail elsewhere.
Broad does have WDL workflows for these but they are pretty messy if you ask me (see here) and are no longer maintained