phasingBam

Introduction

Once SNPs have been phased into whole-chromosome haplotypes, they can be used to phase sequencing reads generated for the same individual using any other sequencing omic profiling (e.g., RNA-seq, ChIP-seq, ATAC-seq, etc.). We implemented a command line tool, phasingBam.sh, to split aligned reads (unphased.bam) into haplotype-specific reads (Hap1.bam, Hap2.bam). This tool was used in our study to generate haplotype-specific signals for different omics (other than Hi-C) across multiple cell lines.

Usage

We provide a one-line command for this process:

conda run -n nHapCUT2 HaploC-tools/bin/phasing_bam.sh -d $wk_dir -b ./path/to/unphased.bam

Examples

conda run -n nHapCUT2 HaploC-tools/bin/phasing_bam.sh -d demo_data -b ./demo_data/bam2phase/WSU_H3K27ac.bam

Output Structure

The output is stored in the same folder where bam2phase is located and consists of bam files from paternal/maternal haplotypes:

|-- WSU_H3K27ac.mat.bam
|-- WSU_H3K27ac.pat.bam
|-- WSU_H3K27ac.mat.bam.bai
`-- WSU_H3K27ac.pat.bam.bai