TOOL

Tool without a name

Name ideas

• Mutations

• Variants

• SNV

• Indel

• Annotation

• Flag

• Filter

• Genotyping

• VAF

• Checker

• Tool

• Pipeline

• SMuRF

How to run

Input

The vcf file must be zipped by bgzip and indexed by tabix

> /hpc/local/CentOS7/pmc_vanboxtel/bin/samtools-bcftools-htslib-1.0_x64-linux/bin/bgzip /path/to/<file.vcf>

/hpc/local/CentOS7/pmc_vanboxtel/bin/samtools-bcftools-htslib-1.0_x64-linux/bin/tabix /path/to/<file.vcf.gz>

Virtual environment

Create new venv

If you need to create a new virtual environment

> virtualenv venv_3.6 -p /hpc/local/CentOS7/common/lang/python/3.6.1/bin/python

Load venv

Before you run the tool, you need load the virtual environment

> . /hpc/pmc_vanboxtel/tools/TOOL/venv_3.6/bin/activate

Install python modules

If you created a new virtual environment, install the required modules

> pip install -r requirements.txt

Run tool

Run the tool

> python /hpc/pmc_vanboxtel/tools/TOOL/tool.py -i /path/to/<file.vcf.gz> -b /path/to/*.bam -c <NAME_OF_CONTROL> -bl /hpc/pmc_vanboxtel/data/Mutation_blacklists/MSC_healthyBM_raw_variants.vcf