A simplified pipeline for ctDNA sequencing data analysis
- BWA: https://github.com/lh3/bwa
- Samtools: https://github.com/samtools/samtools
- VarScan: https://github.com/dkoboldt/varscan
- AfterQC: https://github.com/OpenGene/AfterQC
- dedup.py: https://github.com/OpenGene/dedup
- hg19: http://hgdownload.cse.ucsc.edu/downloads.html
- Annovar: http://annovar.openbioinformatics.org/en/latest/user-guide/startup/
A pair of FastQ files (R1.fq.gz and R2.fq.gz) can be downloaded from http://opengene.org/dataset.html
modify pipeline.sh
according to your local settings, run it.