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USF-HII / snptk

USF HII SNP Toolkit - Analyze and translate SNP entries using NCBI dbSNP and related databases
GNU General Public License v3.0
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Snptk Software Update #5

Closed j2moreno closed 4 years ago

j2moreno commented 4 years ago

  1. Include multi mapping feature in snptk If the SNP ID (rs#) is already in the .bim file, don't take the first rs# based on the position https://github.com/USF-HII/snptk/commit/786ec365ffdf1f0a131ebd53dadef84bf36599dc

  2. Parse GRCh38 json files into flat file for digestion into snptk: https://ftp.ncbi.nih.gov/snp/latest_release/JSON/

  3. Parse GRCh37 vcf files into flat file for digestion into snptk: https://ftp.ncbi.nih.gov/snp/latest_release/VCF/GCF_000001405.25.gz

  4. Parse Rsmerge json file to extract information on merged snps for GRCh37 and GRCh38: https://ftp.ncbi.nih.gov/snp/latest_release/JSON/refsnp-merged.json.bz2

  5. Implement new snptk logic that will omit Snphistory and only use Rsmerge and dbsnp build 153

  6. Integrate hii_plink utility command into snptk https://github.com/USF-HII/hii_plink

countdigi commented 4 years ago

These 6 items should each have there own issue. Its fine to collect them initially in this ticket. As we create issues, we can just link the issue # in the comment here if we want to track them as a whole.

j2moreno commented 4 years ago

Include multi mapping feature in snptk:

countdigi commented 4 years ago

Closing this master ticket - will track in individual issues or Wiki Home Page.