下机数据分析pipeline

这是一篇关于下机数据分析pipeline的思维导图，想要了解下机数据分析pipeline的小伙伴可以收藏起来观看哦

pipeline

• Process sequence
  • clean fq
    • 01 clean.sh
    • 02 fqcheck.sh
  • alignment fq
    • Sentieon.bwamem.sh
• detect germline mutation
  • make duplication
    • Sentieon.mkdup.$samp.sh
  • indel realignment
    • Sentieon.realn.$samp.sh
  • bqsr & call snp, indel
    • Sentieon.bqsr.$samp.sh
  • QC
    • Sentieon.qc.$samp.sh
  • variant annotation
    • variant_Ann.$samp.sh
  • readcount(per 1000bp)
    • bam_readcount.$samp.sh
• calculate QC(ICGC PanCan project)
  • step1
    • flagstat.$samp.sh
  • step2
    • coverageQc.$samp.sh
  • step3
    • genomeCoverage.$samp.sh
  • step4
    • bam_stats.$samp.sh
  • step5
    • summary.$samp.sh
  • step6
    • ContEst.$samp.sh
  • coverage and depth information
    • covdep.$samp.sh
• detect somatic mutation
  • preprocession
    • SplitTarget
      • split_intervals.$TRsplitNum.sh
    • somaticQC
      • somaticQC.sh
  • software
    • TNcallerCalling
      • Sentieon.TNcaller.$samplePair.sh
    • MuTect
      • MuTect.$samplePair.$n.sh
      • MuTect.$samplePair.process.sh
      • annotate
    • MuTect2
      • MuTect2.$samplePair.$n.sh
      • MuTect2.$samplePair.process.sh
      • annotate + mergebed
    • MuSE
      • MuSE.$samplePair.$n.sh
      • MuSE.$samplePair.process.sh
      • annotate + mergebed
    • Strelka2
      • Strelka2.$samplePair.$n.sh
      • Strelka2.$samplePair.process.sh
      • annotate + mergebed
    • SomaticSniper
      • SomaticSniper.$samplePair.sh
      • SomaticSniper.$samplePair.$n.mpileup.sh
      • SomaticSniper.$samplePair.filter.sh
      • annotate + mergebed
    • Lancet
      • Lancet.$samplePair.sh
      • annotate + mergebed
    • Manta
      • Manta.$samplePair.sh
      • Manta.$samplePair.ann.sh
    • Svaba
      • Svaba.$samplePair.sh
      • Svaba.$samplePair.ann.sh
    • Platypus
      • Platypus.$samplePair.$n.sh
      • Platypus.$samplePair.process.sh
    • FACETS
      • FACETS.$samplePair.pileup.sh
      • FACETS.$samplePair.calling.sh"
      • FACETS.$samplePair.ann.sh
    • merge result
      • multTools.$samplePair.sh
      • multTools.$samplePair.ann.sh
• mergebed = $soft.$samplePair.getbed.sh + mergeNonLancetBed.$samplePair.sh
• annotate = $soft.$samplePair.ann.sh