3.3. interhost.py - species and population-level genetic variation¶

This script contains a number of utilities for SNP calling, multi-alignment,

phylogenetics, etc.

usage: interhost.py subcommand

Sub-commands:

snpEff

Undocumented

Annotate variants in VCF file with translation consequences using snpEff.

usage: interhost.py snpEff [-h] [--tmpDir TMPDIR] [--tmpDirKeep]
                           [--loglevel {DEBUG,INFO,WARNING,ERROR,CRITICAL,EXCEPTION}]
                           [--version]
                           inVcf genome outVcf

Positional arguments:

`inVcf`	Input VCF file
`genome`	genome name
`outVcf`	Output VCF file

Options:

`--tmpDir=/tmp`	Base directory for temp files. [default: %(default)s]
`--tmpDirKeep=False`
	Keep the tmpDir if an exception occurs while running. Default is to delete all temp files at the end, even if there’s a failure.
`--loglevel=DEBUG`
	Verboseness of output. [default: %(default)s] Possible choices: DEBUG, INFO, WARNING, ERROR, CRITICAL, EXCEPTION
`--version, -V`	show program’s version number and exit