Qscript Example For Pipelining Gatk With Queue

Question

[newDNASeqer]

I am totally a newbie to Scala/Qscripts. I want to use Queue to automate the multiple steps of running GATK (from Bam to VCF files). Could someone share their QScript examples for achieving this? I want to learn from actual examples. I've found a few examples from https://github.com/broadgsa/gatk/tree/master/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/examples, but I don't think it's really helpful for building my scripts.

Answer 1

[Johan]

I've been working some with QScripts, in our pipeline project called Piper. The code is available here on github: https://github.com/johandahlberg/piper

If you want to start off with some simple example I'd recommend looking at MergeBamsBySample. However, there are some more advanced examples in there as well, including running the GATK best practice data processing pipeline and doing variant calling.