ngs-chew 0.5.1

NGS Chew

NGS Chew

"Tasty, tasty NGS Data!"

NGS Chew is a growing toolbox of software for running quality control and sanity checks on NGS. NGS chew can:

• Create a variant fingerprint file from BAM and VCF/BCF files.
  • The fingerprint files are store efficiently as compressed numpy arrays.
  • Optionally, allele balance information can be stored which enables advanced analysis downstream.
• Compare such fingerprint files to others to detect sample swaps and cryptic relationships.
• Analyze balance-enhanced fingerprint files for detecting cross-sample contamination.

Quickstart

The following will create a sample.npz fingerprint file from the given BAM file.

ngs-chew fingerprint \
    --reference REFERENCE.fasta \
    --output-fingerprint sample.npz \
    --input-bam INPUT.bam \
    --genome-release GRCh37

Changelog

0.5.1 (2022-12-21)

Bug Fixes

• fix for the setup.py based build (#4) (255c848)

0.5.0 (2022-12-21)

Features

• adding README file (#1) (#2) (620d487)

v0.4.0

• Adding plot_var_het.

v0.3.0

• Adding option for writing out VCF file in fingerprinting.
• Adding command plot_aab command for visualizing B allele frequency from VCF files.

v0.2.0

• Adding plot_compare command.

v0.1.1

• Adding --version argument.

v0.1.0

• Everything is new.