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 && cd tblg

2. Install TbLG

pip install .

3. Run TbLG:

tblg -h

Usage

 TbLG (Tuberculosis Lineage Genotyping) | v0.1.4

 Usage: tblg [OPTIONS] [VCF FILES]

 Process one or more VCF files and genotype lineages.

╭─ Arguments ─────────────────────────────────────────────────────────────╮
│ *  VCF_FILES    [VCF FILES]  [required]                                 │
╰─────────────────────────────────────────────────────────────────────────╯
╭─ Options ───────────────────────────────────────────────────────────────╮
│ --output   -o  PATH  Write results to file ['.txt', '.tsv', or '.csv']  │
│ --version  -v        Show the version and exit.                         │
│ --help     -h        Show this message and exit.                        │
╰─────────────────────────────────────────────────────────────────────────╯

• By default, the output is written to the standard output (stdout) in tabular format. However, the user can use the option -o or --output to change the output format to either a tab-separated or comma-separated file.

+----+-------------+-----------+----------------+-----------+------------+-----------+
|    | Sample      | Level 1   | Level 2        | Level 3   | Level 4    | Level 5   |
+====+=============+===========+================+===========+============+===========+
|  0 | SRR16370211 | L2        | L2.2 (ancient) | 2.2.1.2   |            |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+
|  1 | SRR13180266 | L3        | L3.4           |           |            |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+
|  2 | SRR12395111 | L4        | L2.2 (ancient) | L2.2.AA1  |            |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+
|  3 | SRR13180370 | L4        | L4.1           | L4.1.4    |            |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+
|  4 | SRR13180364 | L4        | L4.3           | L4.3.1    |            |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+
|  5 | ERR1203060  | L5        | L5.1           | L5.1.2    |            |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+
|  6 | ERR552796   | M.bovis   |                |           |            |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+

• 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.

+----+-------------+-----------+----------------+-----------+------------+-----------+
|    | Sample      | Level 1   | Level 2        | Level 3   | Level 4    | Level 5   |
+====+=============+===========+================+===========+============+===========+
|  1 | sample_1    | L2        | L2.2 (ancient) | L2.2.AA3  | L2.2.AA3.1 |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+
|  2 | sample_2    | L2*       | L2.1*          |           |            |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+