PMS2_vaR

PMS2_vaR is a framework to assist the inclusion of PMS2 mutational analysis in routine NGS diagnostic pipelines.

Prerequisites

The following tools should be properly installed.

• samtools (v1.10)
• picard (v.2.26.4.jar)
• bwa (0.7.17)
• vardictJava: https://github.com/AstraZeneca-NGS/VarDictJava

Also, R/Bioconductor should be installed with at least these packages: Biostrings, dplyr, httr, jsonlite, optparse, purrr, Rsamtools, stringr, universalmotif, VariantAnnotation, vcfR

How to use

1. Get Code

git clone https://github.com/emunte/PMS2_vaR.git

2. Configure tools.yaml
3. Obtain a modified reference genome file without PMS2CL sequence . This step only needs to be done once.

cd PMS2_vaR
Rscript modify_reference.R [-r --reference reference_genome_path] [-p --pms2CLfasta  full_path_to_PMS2CL_fasta_file] [-o --outputdir path_to_output_directory]

4. Configure vardicjavaParams.yaml

5. Launch PMS2_vaR

cd PMS2_vaR
Rscript run_PMS2_vaR.R [-t tools_file] [-b bam.txt_path] [-r modified_reference_genome_path][-g genome_assembly] [-v vardictjava_path] [-n --samplesname samplesname] [-o --outputdir path_to_output_directory]

Output

An excel file is obtained in the output directory (-o). An algorithm was designed to recommend if a (likely) pathogenic variant would need confirmation by LR-PCR and, if located in PMS2, should be reported