Convert bed file from hg19 to GRCH38

Question

[giulia.cosenza]

Hello everyone! I have a list of over 500,000 rs and I would like to obtain the coordinates (BED file) on the GRCH38 reference genome. I am using the UCSC Table Browser tool, but unfortunately, it doesn't find 90,000 rs, and since there are so many, I cannot manually search for them on sites like Variation Viewer or Gnomad.

Can you suggest how I can obtain the missing 90,000?

Thank you very much.

[Pierre Lindenbaum]

search for your rs in the dbsnp.vcf for grch38 https://ftp.ncbi.nih.gov/snp/latest_release/VCF/ and pulling snps from vcf file using ids

[Ram]

"Convert" is not the right word here. This operation is called a liftover. Search online using this keyword and you'll get started on creating your solution.

Answer 1

[bk11]

You can easily liftover genome coordinates from hg19 to hg38 build using liftOver tool and a chain file. Please check in the link below-

https://genome.sph.umich.edu/wiki/LiftOver