type: cnv_collection
table:
  filename: prepped_variants_for_nstd186.tsv.gz

  chrom:
    column_name: chrom
  pos_begin:
    column_name: pos_beg
  pos_end:
    column_name: pos_end

  chrom_mapping:
    add_prefix: chr


scores:
- id: deletion_duplication 
  column_name: "deletion_duplication"
  type: str
  desc: duplication or deletion
  histogram:
    type: categorical
    y_log_scale: True
    label_rotation: 90
- id: cnv_name 
  column_name: "CNV_name"
  type: str
  desc: "Handy name to refer to the CNV."

meta:
  summary: |
    dbVar CNV collection

  description: |
     
     [dbVar](http://www.ncbi.nlm.nih.gov/dbvar) is a database of genomic structural variations, including deletions, duplications, inversions, and copy number variations (CNVs), collected from human and model organism studies. It provides curated data on variant regions (generalized variation locations) and variant calls (specific observed instances), aiding in understanding genetic diversity and disease associations.


     [Lappalainen et al., DbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Research 2013](https://academic.oup.com/nar/article/41/D1/D936/1068931)
 
     Downloaded on 12/16/2024 from [https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo\_sapiens/by\_study/csv/variants\_for\_nstd186.csv.gz](https://ftp.ncbi.nlm.nih.gov/pub/dbVar/data/Homo_sapiens/by_study/csv/variants_for_nstd186.csv.gz)

     DataPrep.py converts raw file to GRR format. 'Start' and 'Inner Start" columns are consolidated to "pos\_beg"; "End" and "Inner End" columns are consolidated to "pos\_end". 

