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comparison depth_of_coverage.xml @ 4:f244b8209eb8 draft

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bug fix release
author iuc
date Mon, 25 Aug 2014 17:43:11 -0400
parents 340633249b3d
children 35c00763cb5c
comparison
equal deleted inserted replaced
3:2553f84b8174 4:f244b8209eb8
1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="0.0.7"> 1 <tool id="gatk2_depth_of_coverage" name="Depth of Coverage" version="@VERSION@.0">
2 <description>on BAM files</description> 2 <description>on BAM files</description>
3 <expand macro="requirements" /> 3 <expand macro="requirements" />
4 <macros> 4 <macros>
5 <import>gatk2_macros.xml</import> 5 <import>gatk2_macros.xml</import>
6 </macros> 6 </macros>
690 <help> 690 <help>
691 **What it does** 691 **What it does**
692 692
693 DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score. 693 DepthOfCoverage processes a set of bam files to determine coverage at different levels of partitioning and aggregation. Coverage can be analyzed per locus, per interval, per gene, or in total; can be partitioned by sample, by read group, by technology, by center, or by library; and can be summarized by mean, median, quartiles, and/or percentage of bases covered to or beyond a threshold. Additionally, reads and bases can be filtered by mapping or base quality score.
694 694
695 For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html&gt;`_. 695 For more information on the GATK Depth of Coverage, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html&gt;`_.
696 696
697 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_. 697 To learn about best practices for variant detection using GATK, see this `overview &lt;http://www.broadinstitute.org/gatk/guide/topic?name=best-practices&gt;`_.
698 698
699 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_. 699 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
700 700
736 stop int 500 Ending (right endpoint) for granular binning 736 stop int 500 Ending (right endpoint) for granular binning
737 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments. 737 summaryCoverageThreshold int[] [15] for summary file outputs, report the % of bases coverd to >= this number. Defaults to 15; can take multiple arguments.
738 738
739 @CITATION_SECTION@ 739 @CITATION_SECTION@
740 </help> 740 </help>
741 <expand macro="citations" />
741 </tool> 742 </tool>