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 b5113fdea..b38f0fc0b 100644 --- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java +++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java @@ -128,10 +128,12 @@ public class GATKArgumentCollection { @Argument(fullName = "downsample_to_coverage", shortName = "dcov", doc = "Coverage [integer] to downsample to. For locus-based traversals (eg., LocusWalkers and ActiveRegionWalkers)," + "this 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 the " + - "coverage target is an approximate goal that is not guaranteed to be met exactly: the GATK's approach " + - "to downsampling is based on even representation of reads from all alignment start positions, and the " + - "downsampling algorithm will under some circumstances retain slightly more coverage than requested.", + "this controls the maximum number of reads sharing the same alignment start position. 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.", required = false) public Integer downsampleCoverage = null;