How do I check the major allele in a batch by UCSC Genome Browser?
I have a list of genomic positions such as:
chr position
10 97471746
10 97515523
10 97583001
10 97583002
10 97599537
10 97599544
....
I want to check the major allele of each position at the UCSC Genome Browser. I can do that one by one, like, input "10:97471746", then I know this point is "G". BUT my list is too long, I cannot do this one by one manually. Is there a tool or method to do this for a large group of positions simultaneously? Thank you!!!
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WouterDeCoster
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clyumath •
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written
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clyumath •
1 answer
The easiest is probably:
- make a bed file from your positions
- use bedtools getfasta or pyfaidx
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WouterDeCoster
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