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MasonVariator

Generic Workflow Nodes for KNIME: SeqAn version 2.3.2.201707261654 by Freie Universitaet Berlin, Universitaet Tuebingen, and the SeqAn Team

Either simulate variation and write out the result to VCF and optionally FASTA files.

Web Documentation for MasonVariator

Options

version-check
Turn this option off to disable version update notifications of the application.
quiet
Set verbosity to a minimum.
verbose
Enable verbose output.
very-verbose
Enable very verbose output.
seed
The seed to use for the random number generator.
haplotype-name-sep
Haplotype name separator in output FASTA.
no-gen-var-ids
Do not generate variant ids.
num-haplotypes
The number of haplotypes to simulate.
haplotype-sep
The separator between the chromosome and the haplotype name in the output FASTA file.
snp-rate
Per-base SNP rate.
small-indel-rate
Small indel rate.
min-small-indel-size
Minimal small indel size to simulate.
max-small-indel-size
Maximal small indel size to simulate.
sv-indel-rate
Per-base SNP rate.
sv-inversion-rate
Per-base SNP rate.
sv-translocation-rate
Per-base SNP rate.
sv-duplication-rate
Per-base SNP rate.
min-sv-size
Minimal SV size to simulate.
max-sv-size
Maximal SV size to simulate.
methylation-levels
Enable methylation level simulation.
meth-cg-mu
Median of beta distribution for methylation level of CpG loci.
meth-cg-sigma
Standard deviation of beta distribution for methylation level of CpG loci.
meth-chg-mu
Median of beta distribution for methylation level of CHG loci.
meth-chg-sigma
Standard deviation of beta distribution for methylation level of CHG loci.
meth-chh-mu
Median of beta distribution for methylation level of CHH loci.
meth-chh-sigma
Standard deviation of beta distribution for methylation level of CHH loci.

Input Ports

FASTA file with reference. [fasta,fa]
TSV file with variants to simulate. See Section on the Variant TSV File below. [tsv,txt,opt.]
VCF file to write simulated variations to. [vcf]
FASTA file to write simulated haplotypes to. [fasta,fa,opt.]
Path to load original methylation levels from. Methylation levels are simulated if omitted. [fa,fasta,opt.]

Output Ports

TSV file to write breakpoints in variants to. [tsv,txt,Inactive]
Path to write methylation levels to as FASTA. Only written if -of/--out-fasta is given. [fa,fasta,Inactive]

Views

MasonVariator Std Output
The text sent to standard out during the execution of MasonVariator.
MasonVariator Error Output
The text sent to standard error during the execution of MasonVariator. (If it appears in gray, it's the output of a previously failing run which is preserved for your trouble shooting.)

Update Site

To use this node in KNIME, install Generic Workflow Nodes for KNIME: SeqAn from the following update site:

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