Convert bed file from hg19 to GRCH38
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.
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bk11 •
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giulia.cosenza •
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giulia.cosenza •
1 answer
You can easily liftover genome coordinates from hg19 to hg38 build using liftOver tool and a chain file. Please check in the link below-
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"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.