zuoxy ✭

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• Guys, any updated information about the cutoff ? Looking forward to it.

  in StrandOddsRatio computation Comment by zuoxy June 2015
• (Quote) The mutect-1.1.7 seems to work correctly! Many thanks! I have another two questions: 1) Could mutect support multithreading and how could I reduce the total runtime since it require half a month for WES; 2) Could BQSR, indelRealign be perfor…

  in What input files does MuTect accept / require? Comment by zuoxy May 2015
• Hi, I got an error when running on Normal/Tumor bam file: ERROR MESSAGE: java.lang.IllegalArgumentException: Comparison method violates its general contract! below is my command: java -jar muTect-1.1.4.jar --analysis_type MuTect --intervals regio…

  in What input files does MuTect accept / require? Comment by zuoxy May 2015
• Thanks Sheila. But I further want to figure out whether there is any difference on the final vcf between the two workflow: GenotypeGVCFs all samples together then VQSR and GenotypeGVCFs+VQSR per batch then CombineVariants. Does GATK have some worke…

  in what is the best order to use HC, GenotypeVCFs, VariantRecalibrate and CombineVariants? Comment by zuoxy April 2015
• It is indeed a problem of the configuration of java environment on the cluster. Thank you

  in node crash when running GATK on a cluster Comment by zuoxy April 2015