snp database using annotation
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3 months ago
sskimvd • 0

hello For 550,000 SNPs, we only have the chromosomal location or rs number. I would like to annotate ref/alt allele, strand, and frequency information for 550,000 SNPs. I downloaded the GCF_000001405.40.gz file, but there is no strand information. I am curious about a database that contains all ref/alt allele, strand, and frequency information. I think it would be good to download the information that comes up when you search for snp on the gwas catalog website, but I don't know how. I would also really appreciate it if you could tell me how to annotate using a database.

thank you

database gwas snp annotation • 474 views
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I downloaded the GCF_000001405.40.gz file,

what is that file ? where did you downloaded it ?

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you previously asked question that got answers: vcf.gz file Modified ; data prerprocessing coding : review the answer, validate them (ticks on the left)

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3 months ago

https://ftp.ncbi.nih.gov/snp/archive/b156/VCF/GCF_000001405.25.gz is a VCF file.

VCF files are _de_facto_ stranded.

The REF and the ALT allele are the alleles on the fasta REFERENCE sequence GRCh37.p13 .

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Yes but there is no strand information. I also want to annotate strand information about snp.

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as I said, it's a VCF, it's always 5'->3'

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Oh, I missed it, thank you!

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