Changes between Version 47 and Version 48 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
09/05/17 13:40:41 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v47 v48  
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    78 '''Identify and clip  Cigarend Reads and reassign quality scores'''.
     78'''Identify and split  Cigar N Reads and reassign quality scores'''.
    7979
    8080 {{{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}}}