physical position doesn't match

huwenboshi / ImpG

Gaussian imputation of GWAS summary statistics

http://bogdan.bioinformatics.ucla.edu/software/impg/

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physical position doesn't match #8

Open YinLiLin opened 5 years ago

YinLiLin commented 5 years ago

Hi there, I want to impute my summary data of WTCCC1 to 1000Genome, i find the SNPs that share the same names in those tow datasets have different physical position. For example: In WTCCC1: 1 rs4040617 0 819185 G A In 1000Genome: 1 rs4040617 0 779322 G A I don't know why this happened. They are treated as different SNPs when running ImpG, could i just directly replace one of them by another? Thanks in advance.

huwenboshi commented 5 years ago

Hi YinLi,

Sorry for the late reply -- I haven't checked this repository for a while...

We usually recommend to remove both SNPs.

Sincerely,

Huwenbo Shi