Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
help with scala script and SplitNCigarReads
I'm having some trouble getting the arguments to work properly for SplitNCigarReads in a scala script that are specified in article #3891. Specifically:
-rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 and
What I'm trying is something like:
val SNCR = new SplitNCigarReads with CommonArguments SNCR.input_file :+= qscript.bamFile SNCR.out = swapExt(qscript.bamFile, "bam", "split.bam") SNCR.read_filter :+= "ReassignOneMappingQuality -RMQF 255 -RMQT -60" SNCR.unsafe = "ALLOW_N_CIGAR_READS"
The SNCR.unsafe yields a result that indicates:
found : String("ALLOW_N_CIGAR_READS")
and the SNCR.read_filter will work in the dry run, but when I add the -run flag to my scala script it tells me that this argument isn't valid either.
Any thoughts from some scala pros?