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Fix some doc formatting for Depth of Coverage

This commit is contained in:
Christopher Hartl 2011-09-15 21:05:22 -04:00
parent ce73dc4071
commit 9fdf1f8eb6
1 changed files with 9 additions and 0 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
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@ -69,14 +69,23 @@ import java.util.*;
* <h2>Output</h2>
* <p>
* Tables pertaining to different coverage summaries. Suffix on the table files declares the contents:
* </p><p>
* - no suffix: per locus coverage
* </p><p>
* - _summary: total, mean, median, quartiles, and threshold proportions, aggregated over all bases
* </p><p>
* - _statistics: coverage histograms (# locus with X coverage), aggregated over all bases
* </p><p>
* - _interval_summary: total, mean, median, quartiles, and threshold proportions, aggregated per interval
* </p><p>
* - _interval_statistics: 2x2 table of # of intervals covered to >= X depth in >=Y samples
* </p><p>
* - _gene_summary: total, mean, median, quartiles, and threshold proportions, aggregated per gene
* </p><p>
* - _gene_statistics: 2x2 table of # of genes covered to >= X depth in >= Y samples
* </p><p>
* - _cumulative_coverage_counts: coverage histograms (# locus with >= X coverage), aggregated over all bases
* </p><p>
* - _cumulative_coverage_proportions: proprotions of loci with >= X coverage, aggregated over all bases
* </p>
*