Somatic Mutations Rechecker and Filtering

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 SMuRF, you need load the virtual environment

> . /hpc/pmc_vanboxtel/tools/SMuRF/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 SMuRF

Run SMuRF

> python /hpc/pmc_vanboxtel/tools/SMuRF/SMuRF.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_hg38.bed

Known issues

UnicodedDecodeError

Check the encoding of your file

file -bi [FILE]

Convert your vcf file to requested character encoding

> iconv -f iso-8859-1 -t utf8 [FILE] > [OUTPUT]