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PharmGKB / pgkb-ngs-pipeline

PharmGKB NGS Pipeline
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Update GATK version #3

Open kokyriakidis opened 5 years ago

kokyriakidis commented 5 years ago

Is there a reason you use GATK 3.5 instead of the latest 4.1?

markwoon commented 5 years ago

Nope. GATK 4 wasn't even out yet when we were working on this.

Feel free to submit a PR to update it.

kokyriakidis commented 5 years ago

With this pipeline I can get solid results from PharmCAT?

whaleyr commented 5 years ago

That's not really a question with a yes/no answer. This tool helps prepare data for use in PharmCAT but it gives no guarantee of whether or not the PharmCAT tool will give you results of one form or another. If you're interested in the PharmCAT project I recommend reading the docs there and submitting issues if something is unclear or not working as expected.