Changes between Version 5 and Version 6 of SnpCallingPipeline/AlignmentAndCleaning


Ignore:
Timestamp:
Oct 19, 2010 2:59:42 AM (12 years ago)
Author:
Morris Swertz
Comment:

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  • SnpCallingPipeline/AlignmentAndCleaning

    v5 v6  
    2828* lane.chr.covariate_table.csv - table of countcovariates output for recalibration
    2929* lane.chr.recal.bam - alignment map with recalibrated quality scores
    30 == align ==
     30== bwa-align ==
    3131Align each end of paired end.
    3232 
     
    3838[[IncludeSource(ngs_pipelines/templates/ngs/template-paired-end_step_0_1.ftl)]]
    3939
    40 == align-pe ==
     40== bwa-align-pe ==
    4141Align the pairs as one
    4242
     
    7272||docs:    ||http://samtools.sourceforge.net/samtools.shtml ||
    7373
    74 == !MarkDuplicates ==
     74== gatk-!MarkDuplicates ==
    7575Mark duplicate PCR fragments to be filtered in analysis
    7676
     
    8080||docs:    ||http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates ||
    8181
    82 == !IndelRealigner-!KnownsOnly ==
     82== gatk-!IndelRealigner-!KnownsOnly ==
    8383Improve the alignment using known indel information (will reduce false SNP calls)
    8484
     
    8888||docs     ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Running_the_Indel_Realigner_only_at_known_sites ||
    8989
    90 == !FixMateInformation ==
     90== gatk-!FixMateInformation ==
    9191Fix the paired end information as consequence of the realignment.
    9292
     
    9898http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Fixing_Mate_Pairs ||
    9999
    100 == !CountCovariates ==
     100== gatk-!CountCovariates ==
    101101Count covariants, such as machine cycle and bp position, to be used as basis for quality recalibration.
    102102Optionally: plot the results to pdf using AnalyzeCovariates
     
    109109http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration#AnalyzeCovariates.jar ||
    110110
    111 == !TableRecalibration ==
     111== gatk-!TableRecalibration ==
    112112Recalibrate quality scores based on the covariate table
    113113||tool:    ||GenomeAnalysisTK.jar -T TableRecalibration ||