# Variant Designer Nextflow PoC

Short section of the Variant Designer tool.

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## Dependencies
* Singularity - https://github.com/sylabs/singularity
* Dispr - https://github.com/douglasgscofield/dispr

## Description
### Target Region Manifest TSV
Tab separated file detailing the chromosome, start, end and vectors

### MANE Summary
Matched Annotation file - https://www.ncbi.nlm.nih.gov/refseq/MANE/
Transcripts on a genome scale. Updated regularly

### autofill_targeton_manifest.r
Converts the manifest file to be usable downstream in VaLiAnT (Out of scope for PoC). Generates BED files needed in the next steps as well

### generate_bedfiles.sh
Runs Dispr on the BED files. Checks regions against genome for any mismatches

### ClinVar VCF
Variation reference file. Updated weekly

### retrieve_targeton_region_variants.sh
Subsets variation reference file for the target region

### Targeton VCF 
Subset variation file