pici/somatic-variants repository overview

Program list:

• GATK⁠

  java -jar /gatk-protected/target/GenomeAnalysisTK.jar [args]

• Strelka⁠

  strelka2 [args]

• VarScan2⁠

  java -jar /varscan/VarScan.v2.4.2.jar [args]

• Mutect⁠

  java -jar /mutect/target/mutect-1.1.7.jar

• Mutect2⁠

  soon

• samtools⁠

  samtools [args]

• picard⁠

  java -jar /picard-tools-1.140/picard.jar [args]

• sequenza⁠

  Preprocessing

  sequenza-utils.py [args]

  Processing

  R library("sequenza")

• Oncotator⁠

  oncotator [args]

• fastqc⁠

  fastqc [args]

• Java Oracle 7⁠

  java [args]

• Python⁠

  python [args]

• R⁠

  R [args]