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
1 answer
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 .
as I said, it's a VCF, it's always 5'->3'
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what is that file ? where did you downloaded it ?
https://ftp.ncbi.nih.gov/snp/archive/b156/VCF/ I downloaded it from here
you previously asked question that got answers: vcf.gz file Modified ; data prerprocessing coding : review the answer, validate them (ticks on the left)