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LiuzLab / AI_MARRVEL

AI-MARRVEL (AIM) is an AI system for rare genetic disorder diagnosis
GNU General Public License v3.0
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Add gene_only filter script #55

Closed SpicyChicken6 closed 1 month ago

SpicyChicken6 commented 1 month ago

Genomic Region of Interest filter --- Version1 of Gene-Only

NOTE: Promoter upstream 1kb region is not included as requested by Dr.Liu.

What is being added:

Version 1 gene-only scripts for generating GRI filters for hg19 and hg38 genome.

Helpful information:

Data files for bed generation:

  1. Gencode v46 gene annotation
  2. HGMD 2022 database
  3. Clinvar 8/6/2024 database

BED file description:

  1. Version 1 is made of: BED \<--- protein_coding gene + HGMD mutations (50 flanking bp) + Cinvar mutations (50 flanking bp)
  2. Bed file format: chr | start | end
jylee-bcm commented 1 month ago

Great! Can you also upload generated bed files as a comment here? (not git commit),

then I will update it to the shared s3 data dependency!

hyunhwan-bcm commented 1 month ago

Great! Can you also upload generated bed files as a comment here? (not git commit),

then I will update it to the shared s3 data dependency!

A good suggestion, @SpicyChicken6 can you do this?

SpicyChicken6 commented 1 month ago

Great! Can you also upload generated bed files as a comment here? (not git commit),

then I will update it to the shared s3 data dependency!

Sure, it is here: Archive.zip