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

0.9.4 (2024-02-21)

Bug Fixes

• issue with truthiness of numpy array (#70) (698d2a0)

0.9.3 (2024-02-19)

Bug Fixes

• coercing chrX hom/het ratio from None to 0 (#62) (8aaf3ae)
• using previous chrX sites (#64) (#67) (62990a7)

0.9.2 (2024-01-10)

Bug Fixes

• release-please action (#60) (718bd1d)

0.9.1 (2024-01-10)

Bug Fixes

• remove versioneer (Python 3.12+) (#58) (0b3876e)

0.9.0 (2024-01-09)

Features

• add "serve" command (#24) (#35) (56f7078)
• tests with larger (excerpt) datasets (#55) (8ee5421)
• updating sites files for stable RSIDs (#42) (eaef39d)

Bug Fixes

• Fills the stats line (#57) (f74bb70)

Documentation

• adding badges to README (#52) (68c5c82)
• adding sphinx-based documentation (#51) (18ab48b)

0.8.1 (2023-07-18)

Bug Fixes

• sites for GRCh38 (#24) (#39) (79773ef)

0.8.0 (2023-01-16)

Features

• roh calling with "bcftools roh" (#25) (a4af62c)

0.7.1 (2023-01-10)

Bug Fixes

• fixing chrX sites BED files (#22) (c0fb33e)

0.7.0 (2023-01-10)

Features

• collect chrX SNP information for sex identification (#12) (#15) (b210312)
• gather samtools idxstats output (#13) (aafa3cf)
• interpret samtools idxstats output (#18) (50cd8fd)
• using coding regions for chrX sites (#20) (#21) (6c50688)
• write out ngs-chew version to header (#19) (c0f2de5)

Bug Fixes

• use actual peddy formulat for relatedness (#17) (cea0b6c)

0.6.0 (2023-01-02)

Features

• allow writing allele fraction to fingerprint file (#7) (76f1511)

Bug Fixes

• formula for relatedness was off by *2 (#9) (3550dfb)

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.