README.md

ctdna-pipeline

A simplified pipeline for ctDNA sequencing data analysis

prepare the tools

• BWA: https://github.com/lh3/bwa
• Samtools: https://github.com/samtools/samtools
• VarScan: https://github.com/dkoboldt/varscan
• Annovar: http://annovar.openbioinformatics.org/en/latest/user-guide/download/
• AfterQC: https://github.com/OpenGene/AfterQC
• MutScan: https://github.com/OpenGene/MutScan
• GeneFuse: https://github.com/OpenGene/GeneFuse
• dedup.py: https://github.com/OpenGene/dedup
• MrBam: https://github.com/OpenGene/MrBam

prepare the reference data and databases

• hg19: http://hgdownload.cse.ucsc.edu/downloads.html
• Annovar: http://annovar.openbioinformatics.org/en/latest/user-guide/startup/

get data for testing

A pair of FastQ files (R1.fq.gz and R2.fq.gz) can be downloaded from http://opengene.org/dataset.html

test the pipeline

modify pipeline.sh according to your local settings, run it.