Changes between Version 37 and Version 38 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
08/16/17 13:40:44 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v37 v38  
    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'''.
     68 Note, if you are combining multiple experiments in this step the RGSM IDs must be the same while the library IDs must be unique. 
     69
    6770    {{{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}}}