mjakobs / HCMM_CNVs_wrapper

This is a fork of lunching/HCMM_CNVs. This code has been edited to include wrapper functions so it can be run as a command line tool rather than a shiny app.

HCMMCNVs

HCMMCNVs is a browser-based software for detecting copy number variants (CNVs) using whole exome sequencing (WES) technology in combining multiple processed bam inputs with different disease or tumor types.

This repository is a fork of the lunching/HCMM_CNVs repository. This repository contains code that allows HCMM-CNVs to be run as a command line tool, rather than a shiny app.
Please cite the original authors if you use HCMM-CNVs in your work.

Song, C., Su, S.C., Huo, Z., Vural, S., Galvin, J.E. and Chang, L.C., 2021. HCMMCNVs: hierarchical clustering mixture model of copy number variants detection using whole exome sequencing technology. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab183

Requirement

• R >= 4.0.1
• Rsamtools package

Running the HCMM-CNVs wrapper

You will need to provide the following information:

• bedfile: A bed file
• chr: The chromosome that you would like to investigate, e.g. "19". Alternatively, if chr is set to "all", all chromosomes present in the bed file will be analysed.
• bam_directory: A .txt file containing the full path to the bam files that you would like to investigate. One bam file per row - see the input_bams.txt file in the Toy_example folder for proper formatting
• min_coverage: Minimum mean coverage. The default value is "10". HCMM-CNVs will filter regions below the threhold in all samples.
• filename: The name of your analysis
• n_clusters: The number of clusters for the hierarchical clustering step. This should be a value from 2-4. The default value is "3"
• code_dir: The full path to where you have installed HCMM_CNVs_wrapper
• ploidy_file: This should be "1" if you do not have ploidy information, or the path to a file containing your ploidy information.

Make sure R is loaded in your environment and then run the following in the folder in which you would like your results to be stored.

bedfile="/path/to/HCMM_CNVs_wrapper/Toy_example/Demo.bed"
chr="19"
bam_directory="/path/to/HCMM_CNVs_wrapper/Toy_example/input_bams.txt"
min_coverage="10"
filename="Test"
n_cluster="3"
code_dir="/path/to/HCMM_CNVs_wrapper/"
ploidy_file="1"

Rscript --vanilla /path/to/HCMM_CNVs_wrapper/HCMM_CNVs_wrapper.R $code_dir \
$bedfile $chr $bam_directory $min_coverage $filename $n_cluster $ploidy_file