fastQTL no longer normalizes the phenotypes

[aarbduarte]

Hello, I've seen that you removed the option to normalize the phenotypes as was doable by using --normal flag. Was it for a particular motive? Is there any work around? Thank you in advance.

[francois-a]

Hi — No, that option is still there: bin/fastQTL.static --help

[aarbduarte]

additionally when running on nominal pass it finishes alright but when doing permutation it throws an error:

[francois-a]

Can you please run the command (at the bottom) that is throwing the error?

[aarbduarte]

[francois-a]

I meant the command that starts with /home/.../fastQTL

[aarbduarte]

Processing gene [AFE_1_+_43531090_43528756_43538198_Hypothetical]
  * Number of variants in cis = 780
  * Best correlation = 0.2902
  * Number of permutations = 1000 / 1203
gsl: beta.c:44: ERROR: domain error
Default GSL error handler invoked.
Aborted (core dumped)

[francois-a]

That error usually arises when the phenotype lacks complexity (0 or same value in most samples). I'm no longer making changes to fastQTL, but you can either try filtering out such phenotypes, or using tensorQTL, which should be more robust to this.

[aarbduarte]

thank you for your help!