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BRACNAC

BRACNAC (BRAc Copy Number Alteration Caller) is a new tool for calling copy number variations (CNVs) and alterations (CNAs) in BRCA1 and BRCA2 genes.

Installation

Installation from .zip file

unzip BRACNAC.zip
cd BRACNAC

Installation from github

git clone  https://github.com/aakechin/BRACNAC.git
cd BRACNAC

Usage

Windows 7/10

Run executable file BRACNAC.exe

Ubuntu

To use graphical interface run:

python3 main_BRACNAC.py

or in command-line version:

python bracnac.py -in file_with_coverage.csv -af file_with_coordinates.csv -out output_file

BRACNAC can be used with graphical interface or in command-line version. As an input files both versions use:

  • Tab-separated file (TSV) with coverage for each target region (see the detailed description below).
  • TSV-file with coordinates for each target region. They should correspond to target regions of the coverage file.

Other options and input files are optional.

Input file format

  • TSV-file with amplicon coverages should have following columns:

    Patient#, Patient_ID, Barcodes, Median_Coverage, Number_<30, amplicon#1...

Patient_ID, Barcodes, Median_Coverage, Number_<30 are optional columns

Advanced options

  • -ref Reference version (hg19 or hg38). BRCA1 and BRCA2 genome coordinates depend on this version (default: hg19).

  • -notclust Not clust - by default, one of normalization steps includes clusterization of sample coverage values, and normalization is additionally carried out inside sample clusters.

  • -hard_score Hard score threshold - minimal hard score for large rearrangement detection (default: 9.9)

  • -hard_pvalue Hard p-value threshold - maximal p-value for hard filtering mutations (default: 0.001)

  • -score Minimal score for large rearrangement detection (default: 2)

  • -pvalue Maximal p-value for filtering mutations (default: 0.05)

  • -cov Minimal median coverage for patients (default: 100)

  • -perm Number of permutations for calculating p-value (default: 1000)

  • -whole Value for calculating score when whole exon is covered (default: 1)

  • -part Value for calculating score when part of exon is covered (default: 0.5)

  • -non Value for calculating score when exon is not covered (default: 0)

  • -del1 Normalized value of coverage for considering an amplicon as likely deleted (default: 1.3)

  • -del2 Normalized value of coverage for considering an amplicon as probably deleted (default: 1.4)

  • -dupl1 Normalized value of coverage for considering an amplicon as likely duplicated (default: 2.8)

  • -dupl2 Normalized value of coverage for considering an amplicon as probably duplicated (default: 2.7)