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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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Handling chr:positions with more than one snp_id mappings #2

Closed j2moreno closed 4 years ago

j2moreno commented 4 years ago

When using snptk snpid-from-coord we do not handle the case when more than one chr:position maps to multiple snps. Instead we delete these snps causing a large amount of snps to be deleted.

is this behavior wanted? Or do we print both snps and remove from deleted_snps.txt snptk output?

2020-01-16 18:56:58 bionix1.epi.usf.edu DEBUG(1): Has more than one snp_id db[23:104755904] = ['rs2001044', 'rs1199656627']
j2moreno commented 4 years ago

We will be taking the first snp in the chr:position mapping and keeping that value to update plink files. These snps will no longer be deleted.

A separate file will be produced to document chr:positions with mutiple snpid mappings.

Possibly add a mutually exclusive feature to snptk snpid-from-coord that implements this logic above. In that case, we can tell snptk when we want this logic to occur based off different project needs.