comparison reduce_reads.xml @ 4:f244b8209eb8 draft

bug fix release

3:2553f84b8174

<tool id="gatk2_reduce_reads" name="Reduce Reads" version="0.0.7">
  <description>in BAM files</description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>

ReduceReads
Reduces the BAM file using read based compression that keeps only essential information for variant calling

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.

For more information on using read based compression in the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html>`_.

To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_.

If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.

 -noclip_ad / --dont_hardclip_adaptor_sequences ( boolean with default value false )
 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.

@CITATION_SECTION@
  </help>
</tool>

4:f244b8209eb8

<tool id="gatk2_reduce_reads" name="Reduce Reads" version="@VERSION@.0">
  <description>in BAM files</description>
  <expand macro="requirements" />
  <macros>
    <import>gatk2_macros.xml</import>
  </macros>

ReduceReads
Reduces the BAM file using read based compression that keeps only essential information for variant calling

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.

.. For more information on using read based compression in the GATK, see this `tool specific page <http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_compression_reducereads_ReduceReads.html>`_.

To learn about best practices for variant detection using GATK, see this `overview <http://www.broadinstitute.org/gatk/guide/topic?name=best-practices>`_.

If you encounter errors, please view the `GATK FAQ <http://www.broadinstitute.org/gatk/guide/topic?name=faqs>`_.

 -noclip_ad / --dont_hardclip_adaptor_sequences ( boolean with default value false )
 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.

@CITATION_SECTION@
  </help>
  <expand macro="citations" />
</tool>