Changes between Version 64 and Version 65 of BigCompute


Ignore:
Timestamp:
Mar 10, 2011 8:29:01 PM (14 years ago)
Author:
Barbera van Schaik
Comment:

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  • BigCompute

    v64 v65  
    3030
    3131'''Implemented components of the Groningen pipeline'''
    32 ''A more detailed description will follow later''
    33 * !BwaIllumina (''done'') - pe00-bwa-align-pair1.ftl, pe01-bwa-align-pair2.ftl, pe02-bwa-sampe.ftl, pe03-sam-to-bam.ftl, pe04-sam-sort.ftl
    34 * !MarkDuplicates (''done'') - pe05-mark-duplicates.ftl
    35 * PicardQC (''partly done'') - pe04b-picardQC.ftl. Didn't get the R environment up and running yet, so the .pdf .hist and .bamindexstats can not be produced yet. Will continue with the other components and fix this later. Attachment contains info about the required R packages.
    36 * !GatkGenerateIntervalFile (''done'') - see e-mail Freerk on Dec 13, 2010
    37 * !ReAlign (''done'') - pe06-realign.ftl. Works with test dataset, now (9-3-2011) testing with real data
    38 * !FixMates (''done'') - pe07-fixmates.ftl
    39 * !GatkCovariates (''done'') - pe08-covariates-before.ftl, pe11-covariates-after.ftl
    40 * !GatkRecalibrate (''done'') - pe09-recalibrate.ftl
    41 * !SortSam (''done'') - pe10-sam-sort.ftl
    42 * !AnalyzeCovariates (''done'') - pe12-analyze-covariates.ftl
    4332
    44 '''To be implemented'''
    45 * The components of the Groningen pipeline that not implemented as a workflow component yet
    46 * Pindel
     33Template (grid component)
     34
     35''Alignment, realignment, recalibration, stats''
     36* pe0--fastqc.ftl (FastqToFastQC, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/quality/Workflow/FastqToFastQC.gwendia)
     37* pe00-bwa-align-pair1.ftl (!BwaIllumina, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/BwaIllumina.gwendia)
     38* pe01-bwa-align-pair2.ftl (!BwaIllumina, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/BwaIllumina.gwendia)
     39* pe02-bwa-sampe.ftl (!BwaIllumina, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/BwaIllumina.gwendia)
     40* pe03-sam-to-bam.ftl (!BwaIllumina, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/BwaIllumina.gwendia)
     41* pe04a-!HsMetrics.ftl (!CalculateHsMetrics, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/CalculateHsMetrics.gwendia)
     42* pe04b-picardQC.ftl (PicardQC, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/PicardQC.gwendia)
     43* pe04-sam-sort.ftl (!SamSort, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/SamSort.gwendia)
     44* pe05-mark-duplicates.ftl (!MarkDuplicates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/MarkDuplicates.gwendia)
     45* pe06-realign.ftl (!ReAlign, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/ReAlign.gwendia)
     46* pe07-fixmates.ftl (!FixMates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/FixMates.gwendia)
     47* pe08-covariates-before.ftl (!GatkCovariates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/GatkCovariates.gwendia)
     48* pe09-recalibrate.ftl (!GatkRecalibrate, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/GatkRecalibrate.gwendia)
     49* pe10-sam-sort.ftl (!SamSort, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/SamSort.gwendia)
     50* pe11-covariates-after.ftl (!GatkCovariates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/GatkCovariates.gwendia)
     51* pe12-analyze-covariates.ftl (!GatkAnalyzeCovariates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/GatkAnalyzeCovariates.gwendia)
     52
     53''Merge bam per sample and perform SNP and indel calling''
     54* vc00a-unified-genotyper.ftl '''to do'''
     55* vc00b-variant-filtration.ftl '''to do'''
     56* vc00c-variant-eval.ftl '''to do'''
     57* vc00d-picardMetrics.ftl (PicardQC, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/PicardQC.gwendia)
     58* vc00-merge.ftl '''to do'''
     59* vc00.merge.ftl '''to do'''
     60* vc01-coverage.ftl '''to do'''
     61* vc01.unified_genotyper.ftl '''to do'''
     62* vc02.picardQC.ftl (!PicardQC, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/PicardQC.gwendia)
     63* vc02-realigner-target-creator.ftl '''to do'''
     64* vc03.coverage.ftl '''to do'''
     65* vc03-realign.ftl (!ReAlign, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/ReAlign.gwendia)
     66* vc04-fixmates.ftl (!FixMates, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/FixMates.gwendia)
     67* vc05-indel-genotyper-v2.ftl '''to do'''
     68* vc06-filter-indels.ftl '''to do'''
     69* vc07-unified-genotyper.ftl '''to do'''
     70* vc08-make-indel-mask.ftl '''to do'''
     71* vc09-variant-filtration.ftl '''to do'''
     72* vc10-variant-eval.ftl '''to do'''
     73* vc11-name-sort-bam.ftl (!SamSort, lfn://lfc.grid.sara.nl:5010/grid/vlemed/AMC-e-BioScience/Sequence_WF/gvnl/Workflows/SamSort.gwendia)
     74* vc12-pindel.ftl '''to do'''
    4775
    4876'''Data access rights'''