NGS Chew
Project description
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.
- The fingerprint files are store efficiently as compressed
- 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
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
0.9.1 (2024-01-10)
Bug Fixes
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
Documentation
0.8.1 (2023-07-18)
Bug Fixes
0.8.0 (2023-01-16)
Features
0.7.1 (2023-01-10)
Bug Fixes
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
0.6.0 (2023-01-02)
Features
Bug Fixes
0.5.1 (2022-12-21)
Bug Fixes
0.5.0 (2022-12-21)
Features
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.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
ngs-chew-0.9.4.tar.gz
(576.6 kB
view hashes)