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liftOverPlink Syntax error

Hello,

Has anyone used liftOverPlink before? I downloaded the script as well as the chain file, then tried the command below, but it always came up the error message:

python liftOverPlink.py --map mymap.map --out myoutput --chain hg17ToHg18.over.chain.gz
  File "/home/pingwu01/liftOverPlink.py", line 7
    <!DOCTYPE html>
    ^
SyntaxError: invalid syntax

Very confused.. Just wonder if anyone has any clue please? Thanks!

Kitty

snp software error snp
• 1,169 views • link
written by pwuucl • pwuucl

Hello pwuucl,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

• 0 views • link
written by lieven.sterck lieven.sterck

2 answers

From the look of it, your liftOverPlink.py might be a html file. Could you please make sure you have downloaded the file correctly?

Maybe this link will help https://github.com/sritchie73/liftOverPlink/archive/master.zip

• 0 views • link
written by Sam Sam

Many thanks Sam. I was thinking of this as well but struggling to find the right file, your link was very timely! I am using your PRSice2 as well, might ask about the scoring later ... Thanks again

• 0 views • link
written by pwuucl • pwuucl

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