sequence-qc 0.1.2

Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files

sequence_qc

Package for doing various ad-hoc quality control steps from MSK-ACCESS generated FASTQ or BAM files

• Free software: Apache Software License 2.0

• Documentation: https://msk-access.gitbook.io/sequence_qc/

Installation

pip install sequence_qc

Usage

Usage: calculate_noise [OPTIONS]

Calculate noise level of given bam file, across the given positions in bed_file.

Options:

--ref_fasta TEXT

Path to reference fasta, containing all regions in bed_file [required]

--bam_file TEXT

Path to BAM file for calculating noise [required]

--bed_file TEXT

Path to BED file containing regions over which to calculate noise [required]

--threshold FLOAT

Alt allele frequency past which to ignore positions from the calculation

--truncate INTEGER

Whether to exclude trailing bases from reads that only partially overlap the bed file (0 or 1)

--min_mapq INTEGER

Exclude reads with a lower mapping quality

--min_basq INTEGER

Exclude bases with a lower base quality

--help

Show this message and exit.

Versioning

To increase the version number use the following command:

bumpversion (major|minor|patch) --tag

History

0.1.0 (2019-12-06)

• First release on PyPI.