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).
pip install tblgAlternatively:
- Clone TbLG repository:
git clone https://github.com/dbespiatykh/tblg.git && cd tblg- Install TbLG
pip install .- Run TbLG:
tblg -h 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
-oor--outputto 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* | | | |
+----+-------------+-----------+----------------+-----------+------------+-----------+