Generate VCF file with random variants from reference genome
It generates a VCF file with simulated random variants based on the given probability model.
Usage: vcfy [OPTIONS] REFERENCE Generate VCF file with simulated variants in specified range [low, high) for the given region of the reference genome (in FASTA format). In case that the region is not specified the first region is used. If no range is provided, it is assumed that the variants are scattered throughout the region. For more information, consult with the README file. Options: -o, --output FILENAME Write to this file instead of standard output. -m, --mutation-rate FLOAT Base mutation rate. [required] -r, --region TEXT Region ID (default=first region in the reference) -l, --low INTEGER Range lower bound (default=first locus in the region) -h, --high INTEGER Range upper bound (default=last locus in the region) --help Show this message and exit.
Usage: ksnper [OPTIONS] [VCF] Report the number of SNPs in all k-mers. Specify the k and the VCF file, it reports number of SNPS occurred in each k-mer. Options: -o, --output FILENAME Write to this file instead of standard output. -r, --reference FILENAME Reference genome FASTA file. It will be inferred from VCF header, if not specified. -k INTEGER The value of k. [required] -c Set if the input VCF is compressed -d, --dialect [unix|excel-tab|excel] Use this CSV dialect. [default: unix] --help Show this message and exit.
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