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