Mercurial > repos > iuc > gatk2

comparison reduce_reads.xml @ 4:f244b8209eb8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
bug fix release
author iuc
date Mon, 25 Aug 2014 17:43:11 -0400
parents 8bcc13094767
children 35c00763cb5c
comparison
equal deleted inserted replaced
3:2553f84b8174 4:f244b8209eb8
1 <tool id="gatk2_reduce_reads" name="Reduce Reads" version="0.0.7"> 1 <tool id="gatk2_reduce_reads" name="Reduce Reads" version="@VERSION@.0">
2 <description>in BAM files</description> 2 <description>in 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>
152 ReduceReads 152 ReduceReads
153 Reduces the BAM file using read based compression that keeps only essential information for variant calling 153 Reduces the BAM file using read based compression that keeps only essential information for variant calling
154 154
155 This walker will generated reduced versions of the BAM files that still follow the BAM spec and contain all the information necessary for the GSA variant calling pipeline. Some options allow you to tune in how much compression you want to achieve. The default values have been shown to reduce a typical whole exome BAM file 100x. The higher the coverage, the bigger the savings in file size and performance of the downstream tools. 155 This walker will generated reduced versions of the BAM files that still follow the BAM spec and contain all the information necessary for the GSA variant calling pipeline. Some options allow you to tune in how much compression you want to achieve. The default values have been shown to reduce a typical whole exome BAM file 100x. The higher the coverage, the bigger the savings in file size and performance of the downstream tools.
156 156
157 For more information on using read based compression in the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html&gt;`_. 157 .. For more information on using read based compression in the GATK, see this `tool specific page &lt;http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html&gt;`_.
158 158
159 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;`_. 159 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;`_.
160 160
161 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_. 161 If you encounter errors, please view the `GATK FAQ &lt;http://www.broadinstitute.org/gatk/guide/topic?name=faqs&gt;`_.
162 162
221 -noclip_ad / --dont_hardclip_adaptor_sequences ( boolean with default value false ) 221 -noclip_ad / --dont_hardclip_adaptor_sequences ( boolean with default value false )
222 Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired. The program will behave correctly in those cases. 222 Do not hard clip adaptor sequences. Note: You don't have to turn this on for reads that are not mate paired. The program will behave correctly in those cases.
223 223
224 @CITATION_SECTION@ 224 @CITATION_SECTION@
225 </help> 225 </help>
226 <expand macro="citations" />
226 </tool> 227 </tool>