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Frequently asked Questions
1. What is CHERIPIC?
A. CHERIPIC - Computing Homozygosity Enriched Regions In genomes to Prioritize Identification of Candidate variants. As the title suggests, it is a tool written in Ruby that allows to pick causative mutation or variants around the causative from bulks segregant sequencing for genomes with out necessary genetic resources to do Mapping by Sequencing.
2. How does CHERIPIC work?
A. If you have performed a bulk segregant analysis and sequenced your bulks, then you are good to use CHERIPIC. Using a draft assembly or an assembly made from you background (or wild type) bulks, you need to call variants on mutant bulk and background bulk. CHERIPIC takes an assembly used to call variants on your mutant and background bulks and variants files from both bulks as inputs. Using these inputs CHERIPIC calculates variants with homozygosity enrichment score (HMES) and outputs them as a table. Variants with high HMES either contain the causative mutation or be very closely linked to causative mutation.
3. What are the inputs for CHERIPIC?
A. CHERIPIC takes an assembly (in fasta format) that used to call variants on your mutant and background bulks and variants files from both bulks as inputs. Variant files can be of vcf, pileup or bam format.
4. What is the output from CHERIPIC?
A. Output is a tab-delimited file with following information about the variants selected - "HMES, allele frequency, length of contig, id of contig, variant position in contig, reference base, coverage, read bases, base qualities, left sequence to variant, variant allele, right sequence to variant". Left and right sequences are provided to easily design markers and sequence lengths can user adjusted to retrieve enough sequence information.
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