PHASIUS

A tool to visualize phase block structure from (many) BAM, CRAM or VCF files together with BED annotation

Installation

Download a suitable binary from releases.

Install from bioconda: conda install phasius

Or build with cargo: cargo install phasius

Usage

USAGE:
    phasius [OPTIONS] --output <OUTPUT> --region <REGION> <INPUT>...

ARGS:
    <INPUT>...    cram, bam or vcf files to check

OPTIONS:
    -r, --region <REGION>       region string to plot phase blocks from [required]
    -b, --bed <BED>             bed file annotation to use (bgzipped and tabix indexed)
    -t, --threads <THREADS>     Number of crams/bams to parse in parallel [default: 4]
    -d, --decompression <N>     Number of decompression threads to use per cram/bam [default: 1]
    -o, --output <OUTPUT>       HTML output file name
    -h, --help                  Print help information
    -V, --version               Print version information

Example

A dynamic example can be found here

CITATION

If you use this tool, please consider citing our publication.