Home

Links

• dbSNPJson

Todo

• New JSON format
  • Write document how we generate the flat file from NCBI source files with utility https://github.com/USF-HII/snptk#preprocessing-of-ncbi-snp-data
  • GRCh37 (Pending https://github.com/USF-HII/snptk/issues/11)

Complete

• Renamed update-snpid-and-position and snpid-from-coord (map-using-coord and map-using-rs-id)
• Write bin/test-app for snpid-from-coord-update
• Finish https://github.com/USF-HII/snptk/issues/11 (Finish NCBI dbSNP GRCh37 VCF has multiple entries)
  • We have multiple NC entries but running script to determine if its only for X and Y (may be PAR, Pseudo-Autosomal Region)
• Write bin/test-app for update-snpid-and-position
• (KC) Merge update-snpid-and-position and snpid-from-coord-update into new command update-from-map
  • Add option to provide plink command (--plink-path)
  • Add functionality to print command before running (e.g. "run> plink --bfile foo....")
  • Add --dry-run to not execute command
  • The two above will probably use a command function and take dry-run as a kwarg
• (LM) Update remove-duplicates
  • Add option to provide plink command (--plink-path)
  • Add option to provide bcftools command (--bcftools-path)
  • Add functionality to print command before running (e.g. "run> plink --bfile foo....")
  • Add --dry-run to not execute command

Notes