/bwa_pipeline

Genomics pipeline based on Burrows Wheeler Aligment

Primary LanguagePython

BWA pipeline - Genomics pipeline based on BWA (Burrows Wheeler Alignment)

Description

Workflow

Dependencies

  • TrimGalore 0.6.10
  • Picard 2.27.5
  • VarScan >= 2.3.9
  • BWA 0.7.17
  • BCFTools/HtsLib 1.18
  • SAMtools 1.6
  • GATK 4.3.0.0
  • snpEff >= 5.1d
  • Python modules: globalsearch

Running

Edit bwa_config.json for the paths to your data, results and tools. Then execute

./bwa_pipeline.py <directory in data_dir>