Mercurial > repos > iuc > gatk2
comparison depth_of_coverage.xml @ 4:f244b8209eb8 draft
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 <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthOfCoverage.html>`_. | 695 For more information on the GATK Depth of Coverage, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_coverage_DepthOfCoverage.html>`_. |
696 | 696 |
697 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. | 697 To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_. |
698 | 698 |
699 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. | 699 If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_. |
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> |