README.md

Minor variants

This repo contains code for minor variant analysis.

The code can take a BAM file of reads aligned against a reference and compute various statistics related to minor variant detection.

Overview

To open a BAM file, and return a MinorVariantInfo object:

mvi = MinorVariantInfo(bamFile='data/complete-coverage-insertion-sorted.bam')

The MinorVariantInfo object has information about coverage per base (coveragePerBase), the frequency of the most common nucleotide at each position (maxFreqPerBase), as well as methods to compute the mean coverage, the richness, complexity, distance, and nucleotide diversity. It also has a save function to save the computed information as json, which can also be parsed using MinorVariantInfo, which will be much faster than parsing the BAM file.

MinorVariantInfo also takes arguments to specify the minimum base quality and the minimum mapping quality.

A BAM file can also be parsed and saved as json using the script bin/generate-data.py:

$ python bin/generate-data.py --h
usage: generate-data.py [-h] [--sequencingTech SEQUENCINGTECH] [--minBaseQuality MINBASEQUALITY] [--minMappingQuality MINMAPPINGQUALITY] bamFile

Take a bamFile and write MinorVariantInfo.countsPerBase json to stdout.

positional arguments:
  bamFile               A bam file to be analysed.

options:
  -h, --help            show this help message and exit
  --sequencingTech SEQUENCINGTECH
                        The sequencing technology used to create the reads in the bam file.
  --minBaseQuality MINBASEQUALITY
                        Minimum base quality. Bases below the minimum quality will not be output.
  --minMappingQuality MINMAPPINGQUALITY
                        Only use reads above a minimum mapping quality.