Avatar

Hsu Pei-Chun

  • Total activity 12
  • Last activity
  • Member since
  • Following 0 users
  • Followed by 0 users
  • Votes 0
  • Subscriptions 6

Activity overview

Latest activity by Hsu Pei-Chun
  • Avatar

    Hsu Pei-Chun created a post,

    can't generate .segment.vcf.gz when use PostprocessGermlineCNVCalls

    Answered

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: gatk-4.2.0.0b) Exact command used: gatk PostprocessGermlineCNVCalls --model-shard-path 3_CNV/*-model/ --calls-shard-path...

  • Avatar

    Hsu Pei-Chun created a post,

    fail to execute GermlineCNVCaller

    Answered

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used:  gatk-4.1.9.0b) Exact command used: gatk-4.1.9.0/gatk GermlineCNVCaller --run-mode COHORT -L ../10cohort.filter.annotate...

  • Avatar

    Hsu Pei-Chun created a post,

    fail to execute DetermineGermlineContigPloidy

    Answered

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: gatk:4.1.8.1b) Exact command used: gatk DetermineGermlineContigPloidy -L filter_annotated.interval_list -I cohort1_WGS-Z...

  • Avatar

    Hsu Pei-Chun created a post,

    The missing value in Mutect2 vcf

    a) GATK version used: gatk-package-4.1.8.1-local.jar and gatk-package-4.1.2.0-local.jarb) Exact command used: java -jar -Xmx96G -DGATK_STACKTRACE_ON_USER_EXCEPTION=true ~/tools/gatk-4.1.9.0/gatk-pa...

  • Avatar

    Hsu Pei-Chun created a post,

    The missing value in Mutect2 vcf

    If you are seeing an error, please provide(REQUIRED) : a) GATK version used: gatk-package-4.1.8.1-local.jar and gatk-package-4.1.2.0-local.jarb) Exact command used: java -jar -Xmx96G -DGATK_STACKTR...

  • Avatar

    Hsu Pei-Chun created a post,

    "no suitable codecs found" by using CreateSomaticPanelOfNormals

    a) GATK version I used:  gatk-4.1.8.1b) Exact command used: java -jar ~/tools/gatk-4.1.8.1/gatk-package-4.1.8.1-local.jar CreateSomaticPanelOfNormals -V normals_for_pon_vcf.args -O test.vcf.gzc) En...