François Aguet

RNA-SeQC requires GTF in the format specified at https://www.gencodegenes.org/pages/data_format.html, with a gene > transcript > exon hierarchy in the `feature type` column (additional features like CDS etc are also supported)....

We did not find this to be substantially different for assessing sample quality, and removed this option in v2 for simplicity. Please make sure rRNA intervals are properly defined in...

Hi, are you able to share example files that reproduce the issue?

[pgenlib](https://github.com/chrchang/plink-ng/tree/master/2.0/Python) can be used to load dosages from pgen files into numpy. A simple wrapper is available [here](https://github.com/broadinstitute/tensorqtl/blob/master/tensorqtl/pgen.py).

That should not be the case: https://pypi.org/project/firecloud-dalmatian/#history. Can you please check which version is installed?

Hi, missing genotypes are imputed to the mean, see [here](https://github.com/francois-a/fastqtl/blob/master/src/management.cpp#L238). FYI, an improved QTL mapper is available: [tensorQTL](https://github.com/broadinstitute/tensorqtl).

Yes, missing phenotypes are [mean-imputed](https://github.com/francois-a/fastqtl/blob/47180b9a0ef4e806b9fe7e7830d6f4c1181567a0/src/management.cpp#L254). To avoid this, you either need to filter out phenotypes with missing values, or impute them using an alternate method prior to running fastQTL.

That's correct, you need to use `true_df` for this calculation (see [here](https://github.com/francois-a/fastqtl/blob/master/src/analysisPermutationSequence.cpp#L122)). But the reason for a gene missing from the significant pairs list is likely due to the calculation...

Please consider using [tensorQTL](https://github.com/broadinstitute/tensorqtl) instead, as this will provide the column headers. Documentation about the headers is provided [here](https://github.com/broadinstitute/tensorqtl/blob/master/docs/outputs.md). For the FastQTL outputs, the headers are added in [merge_chunks.py](https://github.com/francois-a/fastqtl/blob/master/python/merge_chunks.py).

Hi @goldenflaw @jackhump I submitted a [PR](https://github.com/davidaknowles/leafcutter/pull/206) that merges the different versions.