title: lorikeet summarise usage ---NAME

lorikeet summarise - Calculate ANI and Fst metrics on a given set of VCF files (version 0.8.2)

SYNOPSIS

lorikeet summarise [FLAGS] [OPTIONS]

DESCRIPTION

lorikeet summarise uses a set of VCF files as input and calculates conANI, popANI, subpopANI, and Fst metrics for the variants in each file. ANI metrics require coverage information to determine the number of shared bases in each sample. VCF files do not provide this information, so the shared base size is just the total size of the genome. In our experience, this doesn't really matter that much as the ANI metrics are quite insensitive when provided low coverage samples anyway. Fst tends to perform better for low and high coverage samples and does not require whole genome coverage information.

FLAGS

-v, --verbose

: Print extra debugging information. [default: not set]

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-q, --quiet

: Unless there is an error, do not print log messages. [default: not set]

OPTIONS

-i, --vcfs PATH ..

: Paths to input VCF files. Can provide one or more.

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-i, --vcfs DIRECTORY

: Paths to input VCF files. Can provide one or more.

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-o, --output-directory DIRECTORY

: Output directory. Folder will contain subfolders for each input VCF [default: ./]

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-t, --threads INT

: Maximum number of threads used. [default: 8]

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--qual-by-depth-filter INT

: The minimum QD value for a variant to have for it to be included in the genotyping or ANI analyses. [default: 25]

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--qual-threshold INT

: The PHRED-scaled quality score threshold for use with ANI calculations. [default: 150]

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--depth-per-sample-filter INT

: Minimum depth of a variant in a sample for that sample to be included in ANI & Fst calculations for that variant. [default: 5]

EXIT STATUS

: Successful program execution.

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: Unsuccessful program execution.

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101

: The program panicked.

AUTHOR

Rhys J. P. Newell, Centre for Microbiome Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology <rhys.newell94 near gmail.com>