yhoogstrate / tacc3-fgfr3-bam-quick-scanner

Quick scan for reads mapped to both TACC3 and FGFR3 in order to find fusions

tacc3-fgfr3-quick-bam-scanner

Scans for reads mapped to both TACC3 and FGFR3, directly from BAM files

What it does

It counts reads that are aligned to both TACC3 and FGFR3. Secondary alignments are excluded.

tacc3-fgfr3-bam-quick-scanner Manuscript

If you like to read more about the application of tacc3-fgfr3-bam-quick-scanner or when using this package for scientific purposes, please read/cite the following manuscript:

10.1093/neuonc/noab231

Youri Hoogstrate, Santoesha A Ghisai, Maurice de Wit, Iris de Heer,
Kaspar Draaisma, Job van Riet, Harmen J G van de Werken, Vincent Bours,
Jan Buter, Isabelle Vanden Bempt, Marica Eoli, Enrico Franceschi,
Jean-Sebastien Frenel, Thierry Gorlia, Monique C Hanse, Ann Hoeben,
Melissa Kerkhof, Johan M Kros, Sieger Leenstra, Giuseppe Lombardi,
Slávka Lukacova, Pierre A Robe, Juan M Sepulveda, Walter Taal,
Martin Taphoorn, René M Vernhout, Annemiek M E Walenkamp, Colin Watts,
Michael Weller, Filip Y F de Vos, Guido W Jenster, Martin van den Bent,
Pim J French.

The EGFRvIII transcriptome in glioblastoma, a meta-omics analysis,

Neuro-Oncology, 2021; noab231,
https://doi.org/10.1093/neuonc/noab231

This will indirectly help me further maintaining this software package.

Thank you in advance, Youri

Usage

git clone https://github.com/yhoogstrate/tacc3-fgfr3-bam-quick-scanner.git
cd tacc3-fgfr3-bam-quick-scanner

virtualenv -p python3 .venv
source .venv/bin/activate
pip install click
pip install pysam
pip install tqdm


./tacc3-fgfr3-bam-quick-scanner.py

Usage: tacc3-fgfr3-quick-bam-scanner.py [OPTIONS] [BAM_FILES]...

Options:
  -r, --reference-build [hg19|hg38]
                                  Used reference genome (needed for precise
                                  TACC3 & FGFR3 coordinates)  [required]

  --help                          Show this message and exit.