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Cloufield / gwaslab

A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
GNU General Public License v3.0
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liftover returning an empty dataframe #109

Closed apalmos closed 1 month ago

apalmos commented 1 month ago

Hi,

I saw this in a pervious issue, but my issue is slightly different. I am trying to liftover from hg38 to hg19, but the function return an empty dataframe.

Here is the dataframe before liftover:

image

Here the the command:

df.liftover(n_cores=3, from_build="38", to_build="19")

And here is the output:

image

Any help would be greatly appreciated!

Cloufield commented 1 month ago

Hi, Based on the STATUS code, I guess probably you need to run .basic_check() before liftover to make sure CHR and POS are in correct data types and ready for liftover. Would you please show the log if running .basic_check() before liftover does not work so that I can pinpoint the problem here. Thanks.

apalmos commented 1 month ago

Hi, Thank you very much for your response - ran the basic check & saw this was indeed a data type issue. Have double-checked all columns and it now works fine!