https://github.com/tobiasrausch/nrex
nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
https://github.com/tobiasrausch/nrex
alignment germline mutations sequencing somatic-mutations somatic-variants structural-variation variant-calling
Last synced: about 1 month ago
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nRex: Germline and somatic single-nucleotide, short indel and structural variant calling
- Host: GitHub
- URL: https://github.com/tobiasrausch/nrex
- Owner: tobiasrausch
- License: mit
- Created: 2014-11-26T11:42:55.000Z (over 10 years ago)
- Default Branch: main
- Last Pushed: 2024-10-17T12:33:46.000Z (7 months ago)
- Last Synced: 2024-10-31T21:35:10.447Z (7 months ago)
- Topics: alignment, germline, mutations, sequencing, somatic-mutations, somatic-variants, structural-variation, variant-calling
- Language: Shell
- Homepage:
- Size: 1.86 MB
- Stars: 12
- Watchers: 3
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# nRex
nRex is a set of script to call germline and somatic single-nucleotide variants, short indels and structural variants. The workflow is primarily for human whole-genome sequencing data (>=30x) using short or long-reads.
## Installing nRex
`git clone --recursive https://github.com/tobiasrausch/nRex.git`
`cd nRex/`
`make all`
## Download reference genome
`cd genome/ && ./prepare_genome.sh`
## Download a haplotype reference panel
`cd refpanel/ && ./download.sh`
`cd maps/ && ./download.sh`
## Optional: VEP annotation of variants
To activate the annotation of variants using VEP, you need to download an offline annotation cache for GRCh38
`make .vep`
## Running nRex for GRCh38
There is a pipeline for short- and long-reads. For short-reads:
`./src/nRex.sh `
and for long-reads:
`./src/nRexLR.sh `
## Postprocessing the output of the pipeline
A few helper scripts to summarize the output of the various tools.
### Aggregating QC statistics across multiple samples
`./src/aggregate.sh table *.qc.summary`
### Summarizing VEP output
To generate a table of annotated variants, you can use
`python3 scripts/vep.py -v sample.vep.bcf`