From d5199db8ec1684a50f067387f3722d123496a64b Mon Sep 17 00:00:00 2001 From: David Roazen Date: Tue, 17 Jan 2012 16:26:16 -0500 Subject: [PATCH] Be explicit about setting the snpEff -onlyCoding option in the pipeline When run without an explicit -onlyCoding option, as we've been doing up to now, snpEff automatically sets -onlyCoding to "true" provided that there is at least one transcript marked as "protein_coding", which will always be the case for us in practice (and indeed, all pipeline runs so far with snpEff 2.0.5 have run with -onlyCoding auto-set to "true"). However, given the disastrous effect on annotation quality setting "-onlyCoding false" has, we wish to be explicit with this option rather than relying on snpEff's auto-detection logic. --- .../broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala b/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala index 259856c17..8660ea757 100644 --- a/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala +++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala @@ -47,12 +47,16 @@ class SnpEff extends JavaCommandLineFunction { @Argument(doc="verbose", required=false) var verbose = true + @Argument(doc="onlyCoding", required=false) + var onlyCoding = true + @Output(doc="snp eff output") var outVcf: File = _ override def commandLine = super.commandLine + required("eff") + conditional(verbose, "-v") + + required("-onlyCoding", onlyCoding.toString) + optional("-c", config) + required("-i", "vcf") + required("-o", "vcf") +