how to correct chromosome number and variant position in a VCF file by the rs#?
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!
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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.