Changes between Version 1 and Version 2 of PipelineCommands


Ignore:
Timestamp:
Jan 25, 2011 9:56:12 AM (11 years ago)
Author:
laurent
Comment:

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  • PipelineCommands

    v1 v2  
    3535java -jar -Xmx3g /tools/picard-tools-1.32/BuildBamIndex.jar \ INPUT=/output/filename.b37_1kg.sorted.bam \ OUTPUT=/output/filename.b37_1kg.sorted.bam.bai \ VALIDATION_STRINGENCY=LENIENT \ TMP_DIR=/local
    3636}}}
    37 '''L6. Calculate QC metrics on alignment using Picard''' (~3.5h)
     37'''L6. Calculate QC metrics on alignment using Picard''' (~3.5h, excluding coverage - currently not working)
    3838
    3939This Step is currently updated as:
     
    5555java -jar -Xmx3g /tools/picard-tools-1.32/CalculateHsMetricsWholeGenome.jar \ INPUT=/output/filename.b37_1kg.sorted.bam \ OUTPUT=/output/filename.b37_1kg.HsMetrics \ BAIT_INTERVALS=/resources//hg19/intervals/GoNL.interval_list \ TARGET_INTERVALS=/resources//hg19/intervals/GoNL.interval_list \ VALIDATION_STRINGENCY=LENIENT \ TMP_DIR=/local
    5656}}}
    57 '''L7. Mark duplicates after alignment'''
     57'''L7. Mark duplicates after alignment''' (~2.5h)
    5858
    5959{{{
    6060java -Xmx4g -jar /tools/picard-tools-1.32/MarkDuplicates.jar \ INPUT=/output/filename.b37_1kg.sorted.bam \ OUTPUT=/output/filename.b37_1kg.dedup.bam \ METRICS_FILE=/output/filename.b37_1kg.dedup.metrics \ REMOVE_DUPLICATES=false ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT \ TMP_DIR=/local
    6161}}}
    62 '''L8. Realignment using knowns only'''
     62'''L8. Realignment using knowns only''' (~2.5h)
    6363
    6464{{{
    6565java -Djava.io.tmpdir=/local -Xmx8g -jar \ /tools/Sting/dist/GenomeAnalysisTK.jar -l INFO -T IndelRealigner \ -U ALLOW_UNINDEXED_BAM -I /output/filename.b37_1kg.dedup.bam \ -targetIntervals /resources//hg19/intervals/realign_intervals_hg19_b37_1kg.intervals \ -R /resources//hg19/indices/b37_1kg.fa \ -D /resources//hg19/dbsnp/dbsnp_129_b37_b37_1kg.rod \ -[B:indels,VCF B:indels,VCF] /resources//hg19/indels/1kg.pilot_release.merged.indels.sites./hg19.b37_1kg.vcf \ -o /output/filename.b37_1kg.realigned.bam -knownsOnly -LOD 0.4 -compress 0
    6666}}}
    67 '''L9. Fix mates after realignment'''
     67'''L9. Fix mates after realignment''' (~2h)
    6868
    6969{{{
    7070java -jar -Xmx6g /tools/picard-tools-1.32/FixMateInformation.jar \ INPUT=/output/filename.b37_1kg.realigned.bam \ OUTPUT=/output/filename.b37_1kg.matefixed.bam \ SORT_ORDER=coordinate VALIDATION_STRINGENCY=SILENT TMP_DIR=/local
    7171}}}
    72 '''L10. Calculate covariates before realignment '''
     72'''L10. Calculate covariates before realignment ''' (~12h - Note that this should be improved using more cores. In test at the moment)
    7373
    7474{{{
    7575java -jar -Xmx2g /tools/Sting/dist/GenomeAnalysisTK.jar -l INFO \ -T CountCovariates -U ALLOW_UNINDEXED_BAM \ -R /resources//hg19/indices/b37_1kg.fa \ --DBSNP /resources//hg19/dbsnp/dbsnp_129_b37_b37_1kg.rod \ -I /output/filename.b37_1kg.matefixed.bam \ -cov ReadGroupcovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate \ -recalFile /output/filename.b37_1kg.matefixed.covariate_table.csv
    7676}}}
    77 '''L11. Recalibrate mate fixed and realigned alignment'''
     77'''L11. Recalibrate mate fixed and realigned alignment''' (~5h)
    7878
    7979{{{
    8080java -jar -Xmx4g /tools/Sting/dist/GenomeAnalysisTK.jar -l INFO \ -T TableRecalibration -U ALLOW_UNINDEXED_BAM \ -R /resources//hg19/indices/b37_1kg.fa -I /output/filename.b37_1kg.matefixed.bam \ --recal_file /output/filename.b37_1kg.matefixed.covariate_table.csv \ --out /output/filename.b37_1kg.recal.bam
    8181}}}
    82 '''L12. Sort and index recalibrated alignment'''
     82'''L12. Sort and index recalibrated alignment''' (~5h)
    8383
    8484{{{
     
    8787java -jar -Xmx3g /tools/picard-tools-1.32/BuildBamIndex.jar \ INPUT=/output/filename.b37_1kg.recal.sorted.bam \ OUTPUT=/output/filename.b37_1kg.recal.sorted.bam.bai \ VALIDATION_STRINGENCY=LENIENT \ TMP_DIR=/local
    8888}}}
    89 '''L13. Calculate covariates after realignment and recalibration'''
     89'''L13. Calculate covariates after realignment and recalibration''' (~12h Note that this should be improved using more cores. In test at the moment)
    9090
    9191{{{
    9292java -jar -Xmx2g /tools/Sting/dist/GenomeAnalysisTK.jar -l INFO \ -T CountCovariates -U ALLOW_UNINDEXED_BAM \ -R /resources//hg19/indices/b37_1kg.fa \ --DBSNP /resources//hg19/dbsnp/dbsnp_129_b37_b37_1kg.rod \ -I /output/filename.b37_1kg.recal.sorted.bam \ -cov ReadGroupcovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate \ -recalFile /output/filename.b37_1kg.recal.covariate_table.csv
    9393}}}
    94 '''L14. Analyze covariates before and after'''
     94'''L14. Analyze covariates before and after''' (Currently not working)
    9595
    9696{{{