ctDNA mutation pipeline

My test ctDNA pipeline. Do not use at your production environment.

External Prerequisites

• bwa v0.7 : http://bio-bwa.sourceforge.net
• samtools v1.x : http://sourceforge.net/projects/samtools/files/samtools
• picard v2.18 : https://broadinstitute.github.io/picard/
• GATK4: https://software.broadinstitute.org/gatk/download/
• Varscan2 : http://varscan.sourceforge.net/

Reference

hg19