From 5a2ef37ead2360bb87f4d74feb225cdffae54e1f Mon Sep 17 00:00:00 2001 From: David Roazen Date: Wed, 16 Oct 2013 15:24:33 -0400 Subject: [PATCH] Tweak dcov documentation to help prevent user confusion Geraldine-approved! --- .../arguments/GATKArgumentCollection.java | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java index e1620c938..17849749e 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -129,19 +129,18 @@ public class GATKArgumentCollection { public Double downsampleFraction = null; /** - * For locus-based traversals (eg., LocusWalkers and ActiveRegionWalkers), downsample_to_coverage controls the - * maximum depth of coverage at each locus. For non-locus-based traversals (eg., ReadWalkers), this controls the - * maximum number of reads sharing the same alignment start position. Note that for ReadWalkers, since -dcov controls - * the maximum number of reads sharing the same alignment start position, you will typically need to use much lower - * dcov values than you would with LocusWalkers to see an effect. Note also that this downsampling option does NOT - * produce an unbiased random sampling from all available reads at each locus: instead, the primary goal of the + * For locus-based traversals (LocusWalkers and ActiveRegionWalkers), downsample_to_coverage controls the + * maximum depth of coverage at each locus. For read-based traversals (ReadWalkers), it controls the + * maximum number of reads sharing the same alignment start position. For ReadWalkers you will typically need to use + * much lower dcov values than you would with LocusWalkers to see an effect. Note that this downsampling option does + * not produce an unbiased random sampling from all available reads at each locus: instead, the primary goal of the * to-coverage downsampler is to maintain an even representation of reads from all alignment start positions when - * removing excess coverage. For a true across-the-board unbiased random sampling of reads, use -dfrac instead. Also - * note that the coverage target is an approximate goal that is not guaranteed to be met exactly: the downsampling - * algorithm will under some circumstances retain slightly more coverage than requested. + * removing excess coverage. For a truly unbiased random sampling of reads, use -dfrac instead. Also note + * that the coverage target is an approximate goal that is not guaranteed to be met exactly: the downsampling + * algorithm will under some circumstances retain slightly more or less coverage than requested. */ @Argument(fullName = "downsample_to_coverage", shortName = "dcov", - doc = "Coverage [integer] to downsample to", + doc = "Coverage [integer] to downsample to per locus (for locus walkers) or per alignment start position (for read walkers)", required = false) public Integer downsampleCoverage = null;