Changes between Version 10 and Version 11 of SnpCallingPipeline


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Timestamp:
Oct 4, 2010 2:18:01 PM (12 years ago)
Author:
freerkvandijk
Comment:

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  • SnpCallingPipeline

    v10 v11  
    207207
    208208To remove duplicate reads after alignment PICARD can be used. This tool can also calculate different metrics on alignment data. Therefore PICARD was installed and tested on an aligned and sorted BAM file. A process overview can be seen in figure 3. This process starts at step 4 of the analysis pipeline and uses the sorted alignment file as input. A complete testrun also was performed on this tool and developed pipeline. The command, results etc. can be found in Complete_Picard_test_run.doc.
    209 
    210209== Remarks & Suggestions ==
    211210There are several other tools which can be implemented into the pipeline, one of these tools is an implementation for Beagle. This tool is only usable in an experimental way at the moment.  The only use cases supported by this interface are:
     
    223222GATK also has the ability to run process in parallel. This option is only supported by a limited amount of tools. It can be imported in every tool using parallelism, more information on this can be found on: http://www.broadinstitute.org/gsa/wiki/index.php/Parallelism_and_the_GATK
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     224
     225To construct the correct read groups after merging BAM files obtained using BWA a patch can be used. The patch can be found here: http://www.broadinstitute.org/gsa/wiki/index.php/BWA_patch_to_generate_read_group
     226In the next version of BWA this patch will be included in the standard BWA version.
    225227= Manuals, help etc =
    226228More information about the GATK can be found at: