Changes between Version 48 and Version 49 of SOP/CallingVariantsRNAseq


Ignore:
Timestamp:
09/05/17 13:53:56 (7 years ago)
Author:
krichard
Comment:

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  • SOP/CallingVariantsRNAseq

    v48 v49  
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     83'''Perform  BaseRecalibration'''. \\
     84Calibration files can be found here for hg38 [https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0 Recalibration Files]\\
     85NOTE:  Calibration Files are only available for a few genomes (Human, Mouse, etc).  \\
     86
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     88 {{{java -jar /usr/local/gatk3/GenomeAnalysisTK.jar -T BaseRecalibrator -R /path/to/genome/fasta -I dedupped.bam -knownSites  /path/to/calibration/files -o recalibration.table}}}
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