A tool to visualize phase block structure from (many) BAM, CRAM or VCF files together with BED annotation
Download a suitable binary from releases.
Install from bioconda: conda install phasius
Or build with cargo: cargo install phasius
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
A dynamic example can be found here
If you use this tool, please consider citing our publication.