Changes between Version 44 and Version 45 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
08/16/17 13:53:08 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v44 v45  
    7474 
    7575 {{{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}}}
     76
     77
     78'''Identify and clip  Cigarend Reads and reassign quality scores'''.
     79
     80 {{{java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T SplitNCigarReads -R /path/to/genome/fasta -I dedupped.bam -o split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS -fixMisencodedQuals}}}