HaploCNV

Introduction

HaploCNV is a method that combines information of raw Hi-C coverage (unphased) and haplotype-specific Hi-C coverage to infer copy number status (CN) at both diploid and haploid level

Usage

HaploC-tools/bin/downstreams.sh --help

Examples

conda run -n nHapCUT2 HaploC-tools/bin/downstreams.sh -d demo_data -k HaploCNV -s 1000000

Parameters:

Name	Description
-d	The working directory for phasing
-k	The module to run, should be one of diffIns, diffComp or HaploCNV
-s	Bin size to run the analysis. Default value: 25000 for diffIns analysis, 100000 for HaploCNV analysis

Output Structure

The output of the workflow is stored in the folder specified by wk_dir and will look like this:

wk_dir/CNV/100kb/
|-- tCN.bedgraph
|-- aCN.mat.bedgraph
|-- aCN.pat.bedgraph
|-- coverage.bulk.bedgraph
|-- coverage.mat.bedgraph
|-- coverage.pat.bedgraph
|-- coverage.ratio.mat.bedgraph
|-- coverage.ratio.pat.bedgraph

`-- HaploCNV.rds

File description:

Name	Description
tCN.bedgraph	unphased CNV
aCN.mat.bedgraph	resolved CNV of hap1
aCN.pat.bedgraph	resolved CNV of hap2
coverage.bulk.bedgraph	Hi-C coverage of unphased Hi-C map
coverage.mat.bedgraph	Hi-C coverage of phased Hi-C map hap1
coverage.pat.bedgraph	Hi-C coverage of phased Hi-C map hap2
coverage.ratio.mat.bedgraph	Hi-C coverage ratio of hap1
coverage.ratio.pat.bedgraph	Hi-C coverage ratio of hap2