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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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Snp found in NCBI dbSNP GRCh37 not found in GRCh38 #16

Open j2moreno opened 4 years ago

j2moreno commented 4 years ago

While checking ImmunoChip mapping using snptk, I found that a few snps were deleted that exist in dbSNP (online). 

==> tmp/map-using-rs-id/deleted_snps.txt <==
rs543945992
rs28564600
$ zgrep -w rs543945992 /shares/hii/bioinfo/ref/ncbi/snp/archive/b153/VCF/GCF_000001405.25.gz  
NC_000019.9     54980599        rs543945992     A       T       .       .       RS=543945992;dbSNPBuildID=142;SSR=0;GENEINFO=CDC42EP5:148170;VC=SNV;INT;GNO;FREQ=1000Genomes:0.9998,0.0001997

While rs543945992 exists in the original GRCh37 VCF file, it does not exist in GRCh38. Therefore, when using the script bin/snptk-map-grch37-chromosomes.py to update chromosomes, rs543945992 is thrown away due to not being able to assign correct chromosome designation.

Is this logic okay moving forward?

parikhhm commented 4 years ago

Yes, if we can't map to GRCh38. Let's delete the SNP.