guocy

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guocy
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Beijing
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  • thank you, the problem is resolved.
    in runtime error Comment by guocy July 2015
  • -rw-r--r-- 1 liangl mishl_group 593020157 Jun 25 17:37 ZFY_aln_pe_dedup_realign_recal_rawU_snp_indel2.vcf -rw-r--r-- 1 liangl mishl_group 11827810 Jun 25 20:21 ZFY_aln_pe_dedup_realign_recal_rawU_snp_indel2.vcf.idx -rw-r--r-- 1 liangl mishl_…
    in runtime error Comment by guocy June 2015
  • Hi, I re-run my commend and got a new vcf file, recal file and tranchesfile, however, still did not solve the problem, still show the same error. Please help me on this, I don't know what to do...Thank you so much
    in runtime error Comment by guocy June 2015
  • which vcf you mean that I should delete, there is only the input file is vcf and I delete it from commend, it still shows the same error
    in runtime error Comment by guocy June 2015
  • my command is : /software/biosoft/software/jdk1.7.0_72/bin/java -Xmx45g -jar /leofs/mishl_group/liangl/bin/gatk/GenomeAnalysisTK.jar -T ApplyRecalibration -R /leofs/mishl_group/liangl/ZFY/ref/ucsc.hg19.fasta -input ZFY_aln_pe_dedup_realign_recal_r…
    in runtime error Comment by guocy June 2015