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nrex

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

https://github.com/tobiasrausch/nrex

Science Score: 26.0%

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Keywords

alignment germline mutations sequencing somatic-mutations somatic-variants structural-variation variant-calling
Last synced: 6 months ago · JSON representation

Repository

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

Basic Info
  • Host: GitHub
  • Owner: tobiasrausch
  • License: mit
  • Language: Shell
  • Default Branch: main
  • Homepage:
  • Size: 1.87 MB
Statistics
  • Stars: 12
  • Watchers: 2
  • Forks: 2
  • Open Issues: 0
  • Releases: 1
Topics
alignment germline mutations sequencing somatic-mutations somatic-variants structural-variation variant-calling
Created about 11 years ago · Last pushed 10 months ago
Metadata Files
Readme License Zenodo

README.md

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 <output prefix> <sample1.read1.fq.gz> <sample1.read2.fq.gz>

and for long-reads:

./src/nRexLR.sh <output prefix> <sample.fq.gz>

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

Owner

  • Name: Tobias Rausch
  • Login: tobiasrausch
  • Kind: user
  • Location: Germany
  • Company: EMBL

Researcher in Computational Genomics

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