Usage Guide

This section defines all the available options for running Clade-o-matic.

As a reminder, to get full help for a command use one of:

cladeomatic command -h
cladeomatic command --help

Main Options

One of the main menu options below must be selected

Argument	Description
create	Define lineages and create a kmer scheme
gentoype	Call genotypes from a VCF and a scheme file
benchmark	Test developed scheme using labeled samples and scheme
namer	Rename genotypes within a scheme

Create Scheme

De novo tree data basic usage, ensure the --in_nwk option is selected:

cladeomatic create --in_nwk examples/small_test/tree.nwk  --in_var examples/small_test/snps.vcf --in_meta examples/small_test/sample.meta.txt --outdir small_test_cladeomatic/ --root_name root.0 --reference examples/small_test/root.gbk

Group data basic usage, ensure the --in_groups option is selected:

cladeomatic create --in_groups examples/small_test/groups.tsv --in_var examples/small_test/snps.vcf --in_meta examples/small_test/sample.meta.txt --outdir small_test_cladeomatic_groups/ --root_name root.0 --reference examples/small_test/root.gbk

Create Scheme Options

Argument	Required	Description	Input type	Default Value
--in_var	True	Either Variant Call SNP data (.vcf) or TSV SNP data (.txt)	String
--in_nwk	False	Newick Tree of strains	String
--in_groups	False	Tab delimited file of genotypes	String
--in_meta	True	Tab delimited file of metadata	String
--reference	True	Reference genbank or fasta sequence from VCF	String
--outdir	True	Output Directory to put results	String
--prefix	False	Prefix for output files	String	cladeomatic
--root_name	False	Name of sample to root tree	String
--root_method	False	Method to root tree (midpoint,outgroup)	String
--klen	False	kmer length	Integer	18
--min_members	False	Minimum number of members for a clade to be valid	Integer	1
--min_snp_count	False	Minimum number of unique SNPs for a clade to be valid	Integer	1
--max_snp_count	False	Maximum number of SNPs to be selected for defining each genotype to prevent large numbers of redundant SNPs	Integer	1
--min_perc	False	Minimum percentage of clade members to be positive for a kmer to be valid	Float	0.1
--max_site_ambig	False	Maximum percentage of input sequences which can be missing a site for it to still be valid	Float	0.25
--max_states	False	Maximum number of states for a position [A,T,C,G,N,-]	Integer	6
--max_ambig	False	Maximum number of ambiguous bases allowed in a kmer	Integer	0
--rcor_thresh	False	Correlation coefficient threshold	Float	0.4
--delim	False	Genotype delimiter in group file	String
--num_threads	False	Number of threads to use	1
--no-plots	False	Disable plotting		True
--keep_tmp	False	Keep interim files		True
--debug	False	Show debug information		True
--resume	False	Resume previous analysis		True
--no_compression	False	Skip compression of tree hierarchy		True
--force	False	Force overwrite of existing results directory		True
-V	False	Provide the version number for this build
--version	False	Provide the version number for this build

Genotyping

Basic usage options:

cladeomatic genotype --in_var examples/small_test/snps.vcf --in_scheme examples/small_test/cladeomatic-snp.scheme.txt --sample_meta examples/small_test/sample.meta.txt --genotype_meta examples/small_test/genotype.meta.txt --outfile genotype.calls.txt

Genotyping Options

Argument	Required	Description	Input type	Default Value
--in_var	True	Either Variant Call SNP data (.vcf) or TSV SNP data (.txt)	String
--in_scheme	True	Tab delimited scheme file produced by clade-o-matic	String
--sample_meta	True	Tab delimited sample metadata	String
--genotype_meta	False	Tab delimited genotype metadata	String
--outfile	True	Output Directory to put results	String
--max_missing_positions	False	Maximum number of missing positions for the genotype	Integer	1
--num_threads	False	Number of threads to use	Integer	1
-V	False	Provide the version number for this build
--version	False	Provide the version number for this build

Benchmark Scheme:

Basic usage options:

cladeomatic benchmark --in_var examples/small_test/snps.vcf --in_scheme examples/small_test/cladeomatic-kmer.scheme.txt --in_genotype examples/small_test/genotype.calls.txt --submitted_genotype_col genotype --predicted_genotype_col predicted_genotype  --outdir benchmark

Benchmarking Options

Argument	Required	Description	Input type	Default Value
--in_genotype	True	Genotype report made by genotyper	String
--in_var	True	Either Variant Call SNP data (.vcf) or TSV SNP data (.txt)	String
--in_scheme	True	Tab delimited scheme file produced by clade-o-matic	String
--submitted_genotype_col	True	Name of column containing submitted genotype	String
--predicted_genotype_col	True	Name of column containing predicted genotype	String
--outdir	True	Output Directory to put results	String
--prefix	False	Output Directory to put results	String	cladeomatic
--debug	False	Show debug information		True
-V	False	Provide the version number for this build
--version	False	Provide the version number for this build

Namer

Basic usage options:

Namer Options

Argument	Required	Description	Input type	Default Value
--in_scheme	True	Cladeomatic scheme file	String
--in_name	True	Tab delimited file of (node, name)	String
--outfile	True	Output file for updated scheme	String
-V	False	Provide the version number for this build
--version	False	Provide the version number for this build