TensorQTL Mapping - permutation p values for all associations

Question

[Paula]

Hi everyone,

I have a, maybe rather simple, question on TensorQTL Mapping:

What I want to do:

Run a cis Mapping, getting all cis-associations between variants and genes as an output file, including permutation/beta approximated p values.

What I get:

For each gene just the variant with the top association to this gene is saved in the output file. If I run cis_nominal mode I get all associations printed in the output file, but of course without permutation/beta approximated p values.

My Question:

Does anyone knows, if there is a possibility to get an outout file containing all cis variant-gene associations, not just the top one, with calculated beta-approximated p values?

Thanks a lot in advance!

[Paula]

If there is no option to save permutation p-values for more than one association per gene - why is this permutation schema then implemented? I thought the big improvement of TensorQTL is this permutation way as a multiple testing correcting method...