epitope_diversity

This tool can calculate the diversity (e.g. Shannon entropy and nucleotide diversity) at haplotype level within a specifed region (e.g. epitope) from a NGS sample. It accepts a alignment BAM file, and a GFF3 file as input and returns a tsv result. The application of this tool can be extended to any genomic regions, not only for immune epitopes. Written in Rust, presumably fast-running and memory-efficient.

Usage

epitope_diversity 0.1.1
Haogao Gu <koohoko@gmail.com>
A tool for estimating haplotype diversity of specific regions (e.g. epitopes) from a NGS alignment.

USAGE:
    epitope_diversity [OPTIONS] --bam_file <FILE> --pos_file <FILE>

OPTIONS:
    -f, --bam_file <FILE>      Path of BAM file. Must be accompanied with the BAI index file in the
                               same directory.
    -p, --pos_file <FILE>      Path to a GFF3 file specifying genomic positions of interest.
                               Start/End positions should be 1-based rather than 0-based, and should
                               correspond to the positions in the reference sequence used in SAM/BAM
                               alignment.
    -o, --out_file <NUMBER>    Path to write to the outfile, if "-" will write to stdout. [default:
                               -]
    -v, --verbose              Add this flag to also print text results to stderr.
    -h, --help                 Print help information
    -V, --version              Print version information

Examples:

Example input files

Please check here. These example data are retrieved from test files from IRMA.

Example command and example output

epitope_diversity -f ./examples/A_NP.bam -p "./examples/example.gff" -o -

seqid   start   end     num_of_full_cover_reads num_of_haplotypes    Shannon_entropy population_nucleotide_diversity
A_NP    1096    1112    28      10      1.924832680792314    0.024084633853541412
A_NP    100     120     16      8       2.216917186688699    0.022321428571428572
A_NP    10      1110    No haplotype    No haplotypeNo haplotype

Installation

1. Executable

Directly download executables from Releases.

2. Install from source

1. Install Rust from here.
2. Download source code by git clone https://github.com/Koohoko/epitope_diversity.git.
3. Install with cargo install --path epitope_diversity.
4. You are ready to go.

Details

Description of the methods can be found in this blog post.

Specifically, we used the excat "Shannon entropy" and "Population nucleotide diversity" without normalization/correction in this paper, where

Changelog

• v0.1.1 add columns in the output file for number of haplotypes, and number of total full-cover reads.

TODO

• None

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