I have a list of genomic positions (millions) and I need to get their rsid. I've seen very old posts (~7 years old) on how to do this but I'm afraid they're outdated (using old versions of dbsnp).
Where can I get the most updated version of dbsnp in bed format? If it's not available how can I convert it to bed? I've also read about an issue in new versions where it doesn't give the chromosome name but something like this: CM000663.1.
Thanks for your help!
$ wget -q -O - "https://ftp.ncbi.nih.gov/snp/redesign/pre_build152/organisms/human_9606_b151_GRCh37p13/VCF/00-All.vcf.gz" | bcftools query -f '%CHROM\t%POS0\t%END\t%ID\n'
1 10018 10020 rs775809821
1 10038 10039 rs978760828
1 10042 10043 rs1008829651
1 10050 10051 rs1052373574
1 10050 10051 rs1326880612
1 10054 10055 rs768019142
1 10054 10055 rs892501864
1 10062 10063 rs1010989343
1 10066 10067 rs1489251879
1 10076 10077 rs1022805358
Thanks! Just for future use, how do you know this is the last version of dbsnp? where can I find this information? This file seems to be from 2018.
Latest release is from 2022 and is for GRCh38 (https://ftp.ncbi.nih.gov/snp/latest_release/VCF/ ).
I'm getting this error: [W::vcf_parse] Contig '1' is not defined in the header. (Quick workaround: index the file with tabix.) is this normal behavior?
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