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Either simulate variation and write out the result to VCF and optionally FASTA files.
Options
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. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,embl,embl.bgzf,embl.gz,gbk,gbk.bgzf,gbk.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam,opt.]
Output Ports
- TSV file to write breakpoints in variants to. [tsv,txt]
- Path to write methylation levels to as FASTA. Only written if -of/--out-fasta is given. [fq,fq.bgzf,fq.gz,fastq,fastq.bgzf,fastq.gz,fa,fa.bgzf,fa.gz,fasta,fasta.bgzf,fasta.gz,faa,faa.bgzf,faa.gz,ffn,ffn.bgzf,ffn.gz,fna,fna.bgzf,fna.gz,frn,frn.bgzf,frn.gz,raw,raw.bgzf,raw.gz,sam,sam.bgzf,sam.gz,bam]
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.)
Workflows
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Links
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Developers
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