Simulator for genomic data
Mitty is a data simulator meant to help debug aligners and variant callers.
It requires Python 3.4 or later. It is released under the Apache 2.0 license.
- Generate reads from the whole genome, a single tiny region or from a set of regions as desired
- Handles X, Y chromosomes and polyploidy IF the VCF GT field is properly set
- Read qname stores correct POS, CIGAR and the sizes of variants covered by the read
- Name of sample included in read allowing us to mix FASTQs from
- Can mix viral contamination into reads
- Can do tumor/normal mixes
- Corruption module adds sequencing errors to reads
- Read models can be sampled from existing BAM files
- “God aligner” writes out a BAM with perfect alignments which can be used for BAM comparisons
- Simple genome simulator to generate VCFs with SNPs and different sizes of Insertions and Deletions for aligner/caller testing
- Analyze, plot and debug alignment accuracy with composable analysis functions
Tutorial and usage manual can be found here.
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