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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.
This commit is contained in:
David Roazen 2012-01-17 16:26:16 -05:00
parent 3ba918aff1
commit d5199db8ec
1 changed files with 4 additions and 0 deletions
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4
public/scala/src/org/broadinstitute/sting/queue/extensions/snpeff/SnpEff.scala
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@ -47,12 +47,16 @@ class SnpEff extends JavaCommandLineFunction {
@Argument(doc="verbose", required=false) @Argument(doc="verbose", required=false)
var verbose = true var verbose = true
@Argument(doc="onlyCoding", required=false)
var onlyCoding = true
@Output(doc="snp eff output") @Output(doc="snp eff output")
var outVcf: File = _ var outVcf: File = _
override def commandLine = super.commandLine + override def commandLine = super.commandLine +
required("eff") + required("eff") +
conditional(verbose, "-v") + conditional(verbose, "-v") +
required("-onlyCoding", onlyCoding.toString) +
optional("-c", config) + optional("-c", config) +
required("-i", "vcf") + required("-i", "vcf") +
required("-o", "vcf") + required("-o", "vcf") +