README.md

CASM-Smart-Phase/python

• Installation
  • Without Docker image
• Python Utility Commands
  • generate-bed
  • merge-mnvs

Installation

Without Docker image

• Requires >= python 3.7

# Setup a python virtual environment.
python -m venv /path/to/venv
# Activate python environment
source /path/to/venv/bin/activate
# CD into the python directory
cd CASM-Smart-Phase/python
# Install CASM-Smart-Phase python
pip install ./

Alternatively use the CASM-Smart-Phase Docker container

Python Utility Commands

generate-bed

Generate a bed file of adjacent SNVs in a VCF file. Allows for targeted analysis in smart-phase using the -g option

$ casmsmartphase generate-bed --help
Usage: casmsmartphase generate-bed [OPTIONS]

  Generate a bed file of adjacent SNVs in a VCF for smartphase analysis

Options:
  --version                Show the version and exit.
  -f, --vcfin FILE         Path to input VCF file  [required]
  -o, --output output.bed  Path to write output bed file
  --markhz / --nomarkhz    Mark homozygous adjacent SNVs in the bed file
                           output (default - don't mark)
  --help                   Show this message and exit.

merge-mnvs

Merge MNVs from original VCF using the output from smart-phase

$ casmsmartphase merge-mnvs --help
Usage: casmsmartphase merge-mnvs [OPTIONS]

  Merge MNVs parsed by smartphase into a CaVEMan SNV and MNV vcf file

Options:
  -f, --vcfin FILE                Path to input VCF file  [required]
  -o, --output output.vcf         Path to write output vcf file
  -p, --smart-phased-output sample.phased.output
                                  The phased output file from Smart-Phase
                                  [required]
  -c, --cutoff FLOAT              Exclude any MNVs with a phased score <
                                  cutoff
  -x, --exclude INTEGER           Exclude phased MNV if it matches any of the
                                  exclude flag bits
  --help                          Show this message and exit.