resR SNP Pipeline - A SNP based analysis pipeline

Description

This is a data analysis pipeline based on the unfixed and fixed SNP calling pipelines of https://github.com/MtbEvolution/resR_Project It was modified and augmented for easier configuration, running in various environments and uniform results.

Dependencies

• pandas
• globalsearch
• jinja2
• all the dependencies of resR project
  • VarScan 2.4.0
  • samtools
  • BWA
  • sickle

Usage

./make_snp_calling.py <path to FASTQ files>

TODO:

• avg_sequencing_depth.py: make threshold configurable