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Writing out example to make clear.
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RSWilson1 committed Jan 26, 2024
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To provide bed files for custom gene-level annotation with VEP.
This custom script processes a list of ids (HGNC, transcript) or coordinates with associated annotation, into a comprehensive bed file for the corresponding refseq transcripts for each ID entry.

i.e It could take a list of genes with associated annotation for example Gene A is an oncogene.
It would then find all the corresponding transcripts for that gene and create a bed file for annotating VCFs using VEP. This removes the reliance on picking gene coordinates and directly annotates transcripts
we use for our pipelines.

![Workflow diagram showing TSV containing IDs and annotation to bed file and how it is used in VEP and visualised in IGV using a VCF](https://raw.githubusercontent.com/eastgenomics/gene_annotation2bed/sprint_2/Workflow.png)

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