ngs-chew


Namengs-chew JSON
Version 0.9.3 PyPI version JSON
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home_pagehttps://github.com/bihealth/ngs-chew
SummaryNGS Chew
upload_time2024-02-21 13:28:22
maintainer
docs_urlNone
authorManuel Holtgrewe
requires_python>=3.8
licenseMIT license
keywords bioinformatics
VCS
bugtrack_url
requirements No requirements were recorded.
Travis-CI No Travis.
coveralls test coverage No coveralls. 
            [![CI](https://github.com/bihealth/ngs-chew/actions/workflows/main.yml/badge.svg)](https://github.com/bihealth/ngs-chew/actions/workflows/main.yml)
[![Documentation Status](https://readthedocs.org/projects/ngs-chew/badge/?version=latest)](https://ngs-chew.readthedocs.io/en/latest/?badge=latest)
[![codecov](https://codecov.io/gh/bihealth/ngs-chew/graph/badge.svg?token=DMWFL2WA05)](https://codecov.io/gh/bihealth/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.

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


# Changelog

### [0.9.3](https://www.github.com/bihealth/ngs-chew/compare/v0.9.2...v0.9.3) (2024-02-19)


### Bug Fixes

* coercing chrX hom/het ratio from None to 0 ([#62](https://www.github.com/bihealth/ngs-chew/issues/62)) ([8aaf3ae](https://www.github.com/bihealth/ngs-chew/commit/8aaf3ae80834f91640e7b91b48533bb2cbd95444))
* using previous chrX sites ([#64](https://www.github.com/bihealth/ngs-chew/issues/64)) ([#67](https://www.github.com/bihealth/ngs-chew/issues/67)) ([62990a7](https://www.github.com/bihealth/ngs-chew/commit/62990a7ff026e9ed4102ca79640b989a5e26b8f3))

### [0.9.2](https://www.github.com/bihealth/ngs-chew/compare/v0.9.1...v0.9.2) (2024-01-10)


### Bug Fixes

* release-please action ([#60](https://www.github.com/bihealth/ngs-chew/issues/60)) ([718bd1d](https://www.github.com/bihealth/ngs-chew/commit/718bd1d5fa8f38d6e61e2495870e40fa4ff4f221))

### [0.9.1](https://www.github.com/bihealth/ngs-chew/compare/v0.9.0...v0.9.1) (2024-01-10)


### Bug Fixes

* remove versioneer (Python 3.12+) ([#58](https://www.github.com/bihealth/ngs-chew/issues/58)) ([0b3876e](https://www.github.com/bihealth/ngs-chew/commit/0b3876e598207ee992ea2cec311353e86a08fef2))

## [0.9.0](https://www.github.com/bihealth/ngs-chew/compare/v0.8.1...v0.9.0) (2024-01-09)


### Features

* add "serve" command ([#24](https://www.github.com/bihealth/ngs-chew/issues/24)) ([#35](https://www.github.com/bihealth/ngs-chew/issues/35)) ([56f7078](https://www.github.com/bihealth/ngs-chew/commit/56f70788292a675ea5ee262ca344287d17fab94b))
* tests with larger (excerpt) datasets ([#55](https://www.github.com/bihealth/ngs-chew/issues/55)) ([8ee5421](https://www.github.com/bihealth/ngs-chew/commit/8ee54218fe95f453a75cca391b0a6bd3ee75f627))
* updating sites files for stable RSIDs ([#42](https://www.github.com/bihealth/ngs-chew/issues/42)) ([eaef39d](https://www.github.com/bihealth/ngs-chew/commit/eaef39dd1588939687f98d1daae8310ab344d62b))


### Bug Fixes

* Fills the stats line ([#57](https://www.github.com/bihealth/ngs-chew/issues/57)) ([f74bb70](https://www.github.com/bihealth/ngs-chew/commit/f74bb70cd1f54a42ce9187a053be4f9e228ae689))


### Documentation

* adding badges to README ([#52](https://www.github.com/bihealth/ngs-chew/issues/52)) ([68c5c82](https://www.github.com/bihealth/ngs-chew/commit/68c5c828b434c61454ae55c79b50160561a5c672))
* adding sphinx-based documentation ([#51](https://www.github.com/bihealth/ngs-chew/issues/51)) ([18ab48b](https://www.github.com/bihealth/ngs-chew/commit/18ab48b3b4be4501a216383b42dc9ac85a1ce7c7))

### [0.8.1](https://www.github.com/bihealth/ngs-chew/compare/v0.8.0...v0.8.1) (2023-07-18)


### Bug Fixes

* sites for GRCh38 ([#24](https://www.github.com/bihealth/ngs-chew/issues/24)) ([#39](https://www.github.com/bihealth/ngs-chew/issues/39)) ([79773ef](https://www.github.com/bihealth/ngs-chew/commit/79773ef0e829184e763aee61373ae46f6ea83ed5))

## [0.8.0](https://www.github.com/bihealth/ngs-chew/compare/v0.7.1...v0.8.0) (2023-01-16)


### Features

* roh calling with "bcftools roh" ([#25](https://www.github.com/bihealth/ngs-chew/issues/25)) ([a4af62c](https://www.github.com/bihealth/ngs-chew/commit/a4af62ced20bee37b4342d58aca48aaf9d269e68))

### [0.7.1](https://www.github.com/bihealth/ngs-chew/compare/v0.7.0...v0.7.1) (2023-01-10)


### Bug Fixes

* fixing chrX sites BED files ([#22](https://www.github.com/bihealth/ngs-chew/issues/22)) ([c0fb33e](https://www.github.com/bihealth/ngs-chew/commit/c0fb33e1a7261cfe234dba4938725be6755fb5f1))

## [0.7.0](https://www.github.com/bihealth/ngs-chew/compare/v0.6.0...v0.7.0) (2023-01-10)


### Features

* collect chrX SNP information for sex identification ([#12](https://www.github.com/bihealth/ngs-chew/issues/12)) ([#15](https://www.github.com/bihealth/ngs-chew/issues/15)) ([b210312](https://www.github.com/bihealth/ngs-chew/commit/b210312b40a3aad8e524a8765a8e8b2ef8d0aa8f))
* gather samtools idxstats output ([#13](https://www.github.com/bihealth/ngs-chew/issues/13)) ([aafa3cf](https://www.github.com/bihealth/ngs-chew/commit/aafa3cf7ca94005828c5ce2dd9927d3454291d81))
* interpret samtools idxstats output ([#18](https://www.github.com/bihealth/ngs-chew/issues/18)) ([50cd8fd](https://www.github.com/bihealth/ngs-chew/commit/50cd8fdd72d48bc7330ca5afdb5b108210cc3f75))
* using coding regions for chrX sites ([#20](https://www.github.com/bihealth/ngs-chew/issues/20)) ([#21](https://www.github.com/bihealth/ngs-chew/issues/21)) ([6c50688](https://www.github.com/bihealth/ngs-chew/commit/6c506887f809f9fc834e00f290a17097e6486a67))
* write out ngs-chew version to header ([#19](https://www.github.com/bihealth/ngs-chew/issues/19)) ([c0f2de5](https://www.github.com/bihealth/ngs-chew/commit/c0f2de5ff310410c37d3000533cf45d1c062a520))


### Bug Fixes

* use actual peddy formulat for relatedness ([#17](https://www.github.com/bihealth/ngs-chew/issues/17)) ([cea0b6c](https://www.github.com/bihealth/ngs-chew/commit/cea0b6cda3cfcec795172ef95571458ed74d3cab))

## [0.6.0](https://www.github.com/bihealth/ngs-chew/compare/v0.5.1...v0.6.0) (2023-01-02)


### Features

* allow writing allele fraction to fingerprint file ([#7](https://www.github.com/bihealth/ngs-chew/issues/7)) ([76f1511](https://www.github.com/bihealth/ngs-chew/commit/76f1511e2816ad08e37d76a35a0de02ba9e74c51))


### Bug Fixes

* formula for relatedness was off by *2 ([#9](https://www.github.com/bihealth/ngs-chew/issues/9)) ([3550dfb](https://www.github.com/bihealth/ngs-chew/commit/3550dfb0f35ae85b0e30de74cfda6c8db577bd94))

### [0.5.1](https://www.github.com/bihealth/ngs-chew/compare/v0.5.0...v0.5.1) (2022-12-21)


### Bug Fixes

* fix for the setup.py based build ([#4](https://www.github.com/bihealth/ngs-chew/issues/4)) ([255c848](https://www.github.com/bihealth/ngs-chew/commit/255c8482d1c9d14aadf15de95afaf97140e79205))

## [0.5.0](https://www.github.com/bihealth/ngs-chew/compare/v0.4.0...v0.5.0) (2022-12-21)


### Features

* adding README file ([#1](https://www.github.com/bihealth/ngs-chew/issues/1)) ([#2](https://www.github.com/bihealth/ngs-chew/issues/2)) ([620d487](https://www.github.com/bihealth/ngs-chew/commit/620d48747b845e93533a9f84aff082cc03cb2448))

## 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.

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for detecting cross-sample contamination.\n\n## Quickstart\n\nThe following will create a `sample.npz` fingerprint file from the given BAM file.\n\n```bash\nngs-chew fingerprint \\\n    --reference REFERENCE.fasta \\\n    --output-fingerprint sample.npz \\\n    --input-bam INPUT.bam \\\n    --genome-release GRCh37\n```\n\n\n# Changelog\n\n### [0.9.3](https://www.github.com/bihealth/ngs-chew/compare/v0.9.2...v0.9.3) (2024-02-19)\n\n\n### Bug Fixes\n\n* coercing chrX hom/het ratio from None to 0 ([#62](https://www.github.com/bihealth/ngs-chew/issues/62)) ([8aaf3ae](https://www.github.com/bihealth/ngs-chew/commit/8aaf3ae80834f91640e7b91b48533bb2cbd95444))\n* using previous chrX sites ([#64](https://www.github.com/bihealth/ngs-chew/issues/64)) ([#67](https://www.github.com/bihealth/ngs-chew/issues/67)) ([62990a7](https://www.github.com/bihealth/ngs-chew/commit/62990a7ff026e9ed4102ca79640b989a5e26b8f3))\n\n### [0.9.2](https://www.github.com/bihealth/ngs-chew/compare/v0.9.1...v0.9.2) (2024-01-10)\n\n\n### Bug Fixes\n\n* release-please action ([#60](https://www.github.com/bihealth/ngs-chew/issues/60)) ([718bd1d](https://www.github.com/bihealth/ngs-chew/commit/718bd1d5fa8f38d6e61e2495870e40fa4ff4f221))\n\n### [0.9.1](https://www.github.com/bihealth/ngs-chew/compare/v0.9.0...v0.9.1) (2024-01-10)\n\n\n### Bug Fixes\n\n* remove versioneer (Python 3.12+) ([#58](https://www.github.com/bihealth/ngs-chew/issues/58)) ([0b3876e](https://www.github.com/bihealth/ngs-chew/commit/0b3876e598207ee992ea2cec311353e86a08fef2))\n\n## [0.9.0](https://www.github.com/bihealth/ngs-chew/compare/v0.8.1...v0.9.0) (2024-01-09)\n\n\n### Features\n\n* add \"serve\" command ([#24](https://www.github.com/bihealth/ngs-chew/issues/24)) ([#35](https://www.github.com/bihealth/ngs-chew/issues/35)) ([56f7078](https://www.github.com/bihealth/ngs-chew/commit/56f70788292a675ea5ee262ca344287d17fab94b))\n* tests with larger (excerpt) datasets ([#55](https://www.github.com/bihealth/ngs-chew/issues/55)) ([8ee5421](https://www.github.com/bihealth/ngs-chew/commit/8ee54218fe95f453a75cca391b0a6bd3ee75f627))\n* updating sites files for stable RSIDs ([#42](https://www.github.com/bihealth/ngs-chew/issues/42)) ([eaef39d](https://www.github.com/bihealth/ngs-chew/commit/eaef39dd1588939687f98d1daae8310ab344d62b))\n\n\n### Bug Fixes\n\n* Fills the stats line ([#57](https://www.github.com/bihealth/ngs-chew/issues/57)) ([f74bb70](https://www.github.com/bihealth/ngs-chew/commit/f74bb70cd1f54a42ce9187a053be4f9e228ae689))\n\n\n### Documentation\n\n* adding badges to README ([#52](https://www.github.com/bihealth/ngs-chew/issues/52)) ([68c5c82](https://www.github.com/bihealth/ngs-chew/commit/68c5c828b434c61454ae55c79b50160561a5c672))\n* adding sphinx-based documentation ([#51](https://www.github.com/bihealth/ngs-chew/issues/51)) ([18ab48b](https://www.github.com/bihealth/ngs-chew/commit/18ab48b3b4be4501a216383b42dc9ac85a1ce7c7))\n\n### [0.8.1](https://www.github.com/bihealth/ngs-chew/compare/v0.8.0...v0.8.1) (2023-07-18)\n\n\n### Bug Fixes\n\n* sites for GRCh38 ([#24](https://www.github.com/bihealth/ngs-chew/issues/24)) ([#39](https://www.github.com/bihealth/ngs-chew/issues/39)) ([79773ef](https://www.github.com/bihealth/ngs-chew/commit/79773ef0e829184e763aee61373ae46f6ea83ed5))\n\n## [0.8.0](https://www.github.com/bihealth/ngs-chew/compare/v0.7.1...v0.8.0) (2023-01-16)\n\n\n### Features\n\n* roh calling with \"bcftools roh\" ([#25](https://www.github.com/bihealth/ngs-chew/issues/25)) ([a4af62c](https://www.github.com/bihealth/ngs-chew/commit/a4af62ced20bee37b4342d58aca48aaf9d269e68))\n\n### [0.7.1](https://www.github.com/bihealth/ngs-chew/compare/v0.7.0...v0.7.1) (2023-01-10)\n\n\n### Bug Fixes\n\n* fixing chrX sites BED files ([#22](https://www.github.com/bihealth/ngs-chew/issues/22)) ([c0fb33e](https://www.github.com/bihealth/ngs-chew/commit/c0fb33e1a7261cfe234dba4938725be6755fb5f1))\n\n## [0.7.0](https://www.github.com/bihealth/ngs-chew/compare/v0.6.0...v0.7.0) (2023-01-10)\n\n\n### Features\n\n* collect chrX SNP information for sex identification ([#12](https://www.github.com/bihealth/ngs-chew/issues/12)) ([#15](https://www.github.com/bihealth/ngs-chew/issues/15)) ([b210312](https://www.github.com/bihealth/ngs-chew/commit/b210312b40a3aad8e524a8765a8e8b2ef8d0aa8f))\n* gather samtools idxstats output ([#13](https://www.github.com/bihealth/ngs-chew/issues/13)) ([aafa3cf](https://www.github.com/bihealth/ngs-chew/commit/aafa3cf7ca94005828c5ce2dd9927d3454291d81))\n* interpret samtools idxstats output ([#18](https://www.github.com/bihealth/ngs-chew/issues/18)) ([50cd8fd](https://www.github.com/bihealth/ngs-chew/commit/50cd8fdd72d48bc7330ca5afdb5b108210cc3f75))\n* using coding regions for chrX sites ([#20](https://www.github.com/bihealth/ngs-chew/issues/20)) ([#21](https://www.github.com/bihealth/ngs-chew/issues/21)) ([6c50688](https://www.github.com/bihealth/ngs-chew/commit/6c506887f809f9fc834e00f290a17097e6486a67))\n* write out ngs-chew version to header ([#19](https://www.github.com/bihealth/ngs-chew/issues/19)) ([c0f2de5](https://www.github.com/bihealth/ngs-chew/commit/c0f2de5ff310410c37d3000533cf45d1c062a520))\n\n\n### Bug Fixes\n\n* use actual peddy formulat for relatedness ([#17](https://www.github.com/bihealth/ngs-chew/issues/17)) ([cea0b6c](https://www.github.com/bihealth/ngs-chew/commit/cea0b6cda3cfcec795172ef95571458ed74d3cab))\n\n## [0.6.0](https://www.github.com/bihealth/ngs-chew/compare/v0.5.1...v0.6.0) (2023-01-02)\n\n\n### Features\n\n* allow writing allele fraction to fingerprint file ([#7](https://www.github.com/bihealth/ngs-chew/issues/7)) ([76f1511](https://www.github.com/bihealth/ngs-chew/commit/76f1511e2816ad08e37d76a35a0de02ba9e74c51))\n\n\n### Bug Fixes\n\n* formula for relatedness was off by *2 ([#9](https://www.github.com/bihealth/ngs-chew/issues/9)) ([3550dfb](https://www.github.com/bihealth/ngs-chew/commit/3550dfb0f35ae85b0e30de74cfda6c8db577bd94))\n\n### [0.5.1](https://www.github.com/bihealth/ngs-chew/compare/v0.5.0...v0.5.1) (2022-12-21)\n\n\n### Bug Fixes\n\n* fix for the setup.py based build ([#4](https://www.github.com/bihealth/ngs-chew/issues/4)) ([255c848](https://www.github.com/bihealth/ngs-chew/commit/255c8482d1c9d14aadf15de95afaf97140e79205))\n\n## [0.5.0](https://www.github.com/bihealth/ngs-chew/compare/v0.4.0...v0.5.0) (2022-12-21)\n\n\n### Features\n\n* adding README file ([#1](https://www.github.com/bihealth/ngs-chew/issues/1)) ([#2](https://www.github.com/bihealth/ngs-chew/issues/2)) ([620d487](https://www.github.com/bihealth/ngs-chew/commit/620d48747b845e93533a9f84aff082cc03cb2448))\n\n## v0.4.0\n\n- Adding `plot_var_het`.\n\n## v0.3.0\n\n- Adding option for writing out VCF file in fingerprinting.\n- Adding command `plot_aab` command for visualizing B allele frequency from VCF files.\n\n## v0.2.0\n\n- Adding 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Manuel Holtgrewe
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