Changes between Version 5 and Version 6 of SnpCallingPipeline/AlignmentAndCleaning
- Timestamp:
- Oct 19, 2010 2:59:42 AM (14 years ago)
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SnpCallingPipeline/AlignmentAndCleaning
v5 v6 28 28 * lane.chr.covariate_table.csv - table of countcovariates output for recalibration 29 29 * lane.chr.recal.bam - alignment map with recalibrated quality scores 30 == align ==30 == bwa-align == 31 31 Align each end of paired end. 32 32 … … 38 38 [[IncludeSource(ngs_pipelines/templates/ngs/template-paired-end_step_0_1.ftl)]] 39 39 40 == align-pe ==40 == bwa-align-pe == 41 41 Align the pairs as one 42 42 … … 72 72 ||docs: ||http://samtools.sourceforge.net/samtools.shtml || 73 73 74 == !MarkDuplicates ==74 == gatk-!MarkDuplicates == 75 75 Mark duplicate PCR fragments to be filtered in analysis 76 76 … … 80 80 ||docs: ||http://picard.sourceforge.net/command-line-overview.shtml#MarkDuplicates || 81 81 82 == !IndelRealigner-!KnownsOnly ==82 == gatk-!IndelRealigner-!KnownsOnly == 83 83 Improve the alignment using known indel information (will reduce false SNP calls) 84 84 … … 88 88 ||docs ||http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Running_the_Indel_Realigner_only_at_known_sites || 89 89 90 == !FixMateInformation ==90 == gatk-!FixMateInformation == 91 91 Fix the paired end information as consequence of the realignment. 92 92 … … 98 98 http://www.broadinstitute.org/gsa/wiki/index.php/Local_realignment_around_indels#Fixing_Mate_Pairs || 99 99 100 == !CountCovariates ==100 == gatk-!CountCovariates == 101 101 Count covariants, such as machine cycle and bp position, to be used as basis for quality recalibration. 102 102 Optionally: plot the results to pdf using AnalyzeCovariates … … 109 109 http://www.broadinstitute.org/gsa/wiki/index.php/Base_quality_score_recalibration#AnalyzeCovariates.jar || 110 110 111 == !TableRecalibration ==111 == gatk-!TableRecalibration == 112 112 Recalibrate quality scores based on the covariate table 113 113 ||tool: ||GenomeAnalysisTK.jar -T TableRecalibration ||
