BRCA-PrimaryRecurrent

Scripts for somatic variant calling and allele-specific copy number profiling in matched tumor/normal whole exome sequencing data.

Required Software:

• Python 3.7+
  [https://www.python.org/downloads/]

• vcfpy
  [https://vcfpy.readthedocs.io/en/stable/]

• Snakemake
  [https://snakemake.readthedocs.io/en/stable/getting_started/installation.html]

• samtools
  [https://github.com/samtools/samtools]

• bcftools
  [https://github.com/samtools/bcftools]

• GATK 4
  [https://gatk.broadinstitute.org/hc/en-us/articles/360037593851-Mutect2]

• Strelka2
  [https://github.com/Illumina/strelka]

• VarDictJava
  [https://github.com/AstraZeneca-NGS/VarDict]

• VarScan2
  [https://github.com/dkoboldt/varscan]

• R
  [https://www.r-project.org/]

• Sequenza (R Package)
  [https://cran.r-project.org/web/packages/sequenza/index.html]

• Sequenza-utils
  [https://bitbucket.org/sequenzatools/sequenza-utils/src/master/]

Usage

snakemake -s mutect2.snake --configfile config.yaml
snakemake -s strelka2.snake --configfile config.yaml
snakemake -s vardictjava.snake --configfile config.yaml
snakemake -s sequenza.snake --configfile config.yaml
snakemake -s varscan2.snake --configfile config.yaml

Authors

Jennifer Shah jennshah@pennmedicine.upenn.edu

Brad Wubbenhorst bwubb@pennmedicine.upenn.edu

Paper Citation