I have a very large *.bed file with 15862212 lines from a whole genome VCF. I annotated the VCF for SNPs and now have a file with a preview below using the protocol in C: How to get SNP identifiers from VCF file? . How can I get the descriptors for these rs* IDs? My main goal is to figure out which blood-type I have from this information.
-bash-4.1$ zcat genome.vcf.hg38.snp147.bed.gz | head -n 10
chr1 10019 10020 rs775809821
chr1 10055 10056 rs768019142
chr1 10107 10108 rs62651026 .
chr1 10108 10109 rs376007522 .
chr1 10128 10129 rs796688738
chr1 10138 10139 rs368469931
chr1 10144 10145 rs144773400
chr1 10146 10147 rs779258992
chr1 10149 10150 rs371194064
chr1 10165 10166 rs796884232
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written
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O.rka
1 answer
You can use the ENSEMBL RESTful API in basically any language you'd want. It will return basic info and population frequencies. The Variant Effect Predictor may also be worth your time. I don't think these services will really help though, since blood type is mostly determined by only a handful of variants.
See this page for a lot more info and different sets of variants that may be helpful for you.
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what do you mean with "descriptors" ?
I guess there isn't a descriptor for each snp but to find metadata associated with snps such as: https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=144773400
SNP annotations file: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp142Common.txt.gz