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https://github.com/bioinfo-pf-curie/oncodriver

Detection of driver gene alteration

https://github.com/bioinfo-pf-curie/oncodriver

Science Score: 26.0%

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Repository

Detection of driver gene alteration

Basic Info
  • Host: GitHub
  • Owner: bioinfo-pf-curie
  • Language: Python
  • Default Branch: main
  • Size: 58.6 KB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog

README.md

oncoDriver

Filter and select driver alterations for cancer genes

Usage

``` usage: oncoDriver.py [-h] [-i VCF] [--cnv CNV] --config CONFIG [--sample SAMPLE] [--minvaf MINVAF] [--maxmaf MAXMAF] [--mindepth MINDEPTH] [--minaltdepth MINALTDEPTH] [--usecanonical] [--canonicalids CANONICALIDS] --drivergenes DRIVER_GENES [--output OUTPUT] [--outputcnv OUTPUTCNV] [--verbose] [--debug] [--strict] [--version]

options: -h, --help show this help message and exit -i VCF, --vcf VCF Input file (.vcf, .vcf.gz, .bcf) (default: None) --cnv CNV Input file for CNV (segments.transformedannotoncokb.txt) (default: None) --config CONFIG Decision tree config file (default: None) --sample SAMPLE Specify the sample ID to focus on (default: None) --minvaf MINVAF Filter variants with Allelic Ratio <= vaf (default: None) --maxmaf MAXMAF Filter variants with MAF > maf (default: None) --mindepth MINDEPTH Filter variants with depth < mindepth (default: None) --minaltdepth MINALTDEPTH Filter variants with alternative allele depth <= minaltdepth (default: None) --usecanonical Use canonical transcript only (default: False) --canonicalids CANONICALIDS File with canonical IDs information (default: None) --drivergenes DRIVERGENES Cancer gene list from oncoKB (default: None) --output OUTPUT Output file name (default: None) --outputcnv OUTPUTCNV CNV output file name (default: None) --verbose Active verbose mode (default: False) --debug Export original VCF with ONCODRIVER tag (default: False) --strict Raise an error instead of warnings (default: False) --version Version number

```

Command line

python oncoDriver.py \ --vcf D1326R01_vs_D1326R02_Mutect2_filtered_pass_norm_COSMIC_ICGC_CancerHotspots_GnomAD_dbNSFP.vcf.gz \ --sample D1326R02 \ --config ./config/pathogenic_variants.yml \ --oncoKB_genes ./assets/cancerGeneList.tsv \ --canonical_ids MANE.GRCh38.v1.3.refseq_genomic.gtf.gz \ --use_canonical

Owner

  • Name: Institut Curie, Bioinformatics Core Facility
  • Login: bioinfo-pf-curie
  • Kind: organization
  • Location: Paris, France

bioinformatics platform of the Institut Curie

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