Package: tblg
A command-line tool to genotypeMycobacterium tuberculosislineage from a VCF fileDescriptionThe Tuberculosis Lineage Genotyping (TbLG) is a tool that uses variant call formatVCFfiles to quickly and accurately assign a lineage to isolates of theMycobacterium tuberculosiscomplex (MTBC).InstallationpipinstalltblgAlternatively:CloneTbLGrepository:gitclonehttps://github.com/dbespiatykh/tblg.git&&cdtblgInstallTbLGpipinstall.RunTbLG:tblg-hUsageTbLG(TuberculosisLineageGenotyping)|v0.1.4Usage:tblg[OPTIONS][VCFFILES]ProcessoneormoreVCFfilesandgenotypelineages.

╭─Arguments─────────────────────────────────────────────────────────────╮
│*VCF_FILES[VCFFILES][required]│
╰─────────────────────────────────────────────────────────────────────────╯
╭─Options───────────────────────────────────────────────────────────────╮
│--output-oPATHWriteresultstofile['.txt','.tsv',or'.csv']│
│--version-vShowtheversionandexit.│
│--help-hShowthismessageandexit.│
╰─────────────────────────────────────────────────────────────────────────╯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*          |           |            |           |
+----+-------------+-----------+----------------+-----------+------------+-----------+