how to correct chromosome number and variant position in a VCF file by the rs#?
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7.2 years ago
miaowzai ▴ 390

I have a VCF file that contains some variants with wrong chromosome numbers and wrong positions. For example:

#CHROM  POS ID  REF ALT
0   0   rs25    A   G
25  155233098   rs2037999   T   C

I don't know how this is generated. But all the incorrectly-recorded variants have rs numbers. It's not practical to look for their chromosome number and position one by one. Is there any tool to do this?

Thanks!

rsID VCF • 2.2k views
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If you want to get the position and chromosome of a bunch of rs-numbers you can use the dbSNP batch query.

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