tblg 0.1.0

A command-line tool to genotype Mycobacterium tuberculosis lineage from a VCF file

A command-line tool to genotype Mycobacterium tuberculosis lineage from a VCF file

Description

The Tuberculosis Lineage Genotyping (TbLG) is a tool that uses variant call format VCF files to quickly and accurately assign a lineage to isolates of the Mycobacterium tuberculosis complex (MTBC).

Installation

pip install tblg

Alternatively:

1. Clone TbLG repository:

git clone https://github.com/dbespiatykh/tblg.git

2. Install TbLG

pip install .

3. Run TbLG:

stblg -h

Usage

Usage: tblg [OPTIONS] <vcf_files>

  TbLG (Tuberculosis Lineage Genotyping)

  Process one or more VCF files and genotype lineages.

  VCF_FILES: One or more VCF files to be processed.

Options:
  -o, --output PATH  Write results to file '.txt', '.tsv', or '.csv'.
  -h, --help         Show this message and exit.

• Note: If an asterisk * appears in a 1 or 2 level lineage call, it indicates that the lineage contains only one of two barcoding SNPs.