David Roazen d5199db8ec 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.		2012-01-17 20:04:27 -05:00
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qscript/org/broadinstitute/sting/queue/qscripts	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
src/org/broadinstitute/sting/queue	Be explicit about setting the snpEff -onlyCoding option in the pipeline	2012-01-17 20:04:27 -05:00
test/org/broadinstitute/sting/queue	Updating the MD5s	2011-12-21 15:14:05 -05:00