Where can I download dbsnp in hg19?

Question

[_quantum_girl_]

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 I've seen very old posts (~7 years old) on how to do this but I'm afraid they're outdated (using old versions of dbsnp).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!

Answer 1

[Pierre Lindenbaum]

$ 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

[_quantum_girl_]

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.

[GenoMax]

Latest release is from 2022 and is for GRCh38 (https://ftp.ncbi.nih.gov/snp/latest_release/VCF/ ).

[_quantum_girl_]

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?