Changes between Version 40 and Version 41 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
08/16/17 13:46:20 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v40 v41  
    6565'''2 - Replace ReadGroups, mark duplicate reads , clip intron overhangs and  reassign mapping qualities with[http://broadinstitute.github.io/picard/ Picard Tools]'''
    6666
    67 '''   Replace read groups and order, by coordinates, the reads'''.
     67'''Replace read groups and order, by coordinates, the reads'''.
    6868 Note, if you are combining multiple experiments in this step the RGSM IDs must be the same while the library IDs must be unique. 
    6969
    7070 {{{java -jar /usr/local/share/picard-tools/picard.jar AddOrReplaceReadGroups I=output.sam O=rg_added_sorted.bam SO=coordinate RGID=ID_NAME RGLB=library RGPL=illumina RGPU=identifier RGSM=sample_name}}}
     71
     72'''Mark duplicate reads'''.
     73{{{java -jar /usr/local/share/picard-tools/picard.jar MarkDuplicates I=rg_added_sorted.bam O=dedupped.bam CREATE_INDEX=true VALIDATION_STRINGENCY=SILENT M=output.metrics}}}