vcf2scoary1
Takes in vcf files and creates a presence/absence matrix of mutations in the roary/scoary format
Usage
vcf2scoary [-h]
[--out
OUT]
[--types
TYPES]
[--version]
[--force]
<VCF_file>
Options
positional arguments:
- <VCF_file>
-
The VCF file to convert to Roary/Scoary format
optional arguments:
-
-h, --help -
show this help message and exit
-
--out OUT -
The path to the output file
-
--types TYPES -
The types of variants to include in the output. NOTE: This works if TYPE=XX can be found in the INFO column of the vcf file. The special keyword ALL includes all types. This is the default setting. Common types are snp, mnp, ins, del and complex. Give as comma-separated list. Example:
--typessnp,ins,del
-
--version -
show program's version number and exit
-
--force -
Force overwriting of output file. (If it already exists)
by Ola Brynildsrud ([email protected])
Releases
Unchanged in 4 releases since Debian 10 (Buster).