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Merge pull request #402 from broadinstitute/gg_dcov_docs 

Improvements to gatkdocs related to downsampling
This commit is contained in:
Ryan Poplin 2013-09-27 07:07:21 -07:00
parent cba9668641 511948890a
commit f3a67edc24
2 changed files with 27 additions and 14 deletions
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26
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -119,21 +119,29 @@ public class GATKArgumentCollection {
// Downsampling Arguments
//
// --------------------------------------------------------------------------------------------------------------
@Argument(fullName = "downsampling_type", shortName="dt", doc="Type of reads downsampling to employ at a given locus. Reads will be selected randomly to be removed from the pile based on the method described here", required = false)
/**
* Reads will be selected randomly to be removed from the pile based on the method described here.
*/
@Argument(fullName = "downsampling_type", shortName="dt", doc="Type of reads downsampling to employ at a given locus", required = false)
public DownsampleType downsamplingType = null;
@Argument(fullName = "downsample_to_fraction", shortName = "dfrac", doc = "Fraction [0.0-1.0] of reads to downsample to", required = false)
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
* 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.
*/
@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 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.",
doc = "Coverage [integer] to downsample to",
required = false)
public Integer downsampleCoverage = null;

15
settings/helpTemplates/generic.template.html
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@ -174,11 +174,16 @@
</#if>
<#if downsampling?size != 0>
<h3>Downsampling settings</h3>
<p>This tool overrides the engine's default downsampling settings.</p>
<ul>
<li>Mode: <b>${downsampling.by}</b></li>
<li>To coverage: <b>${downsampling.to_cov}</b></li>
</ul>
<#if downsampling.by == "NONE">
<p>This tool does not apply any downsampling by default.</p>
</#if>
<#if downsampling.by != "NONE">
<p>This tool applies the following downsampling settings by default.</p>
<ul>
<li>Mode: <b>${downsampling.by}</b></li>
<li>To coverage: <b>${downsampling.to_cov}</b></li>
</ul>
</#if>
</#if>
<#if refwindow?size != 0>
<h3>Window size</h3>