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exomiser / Exomiser

A Tool to Annotate and Prioritize Exome Variants
https://exomiser.readthedocs.io
GNU Affero General Public License v3.0
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Empty inheritanceModes leads to empty output tables #481

Closed genetikzentrum closed 1 year ago

genetikzentrum commented 1 year ago

We noticed that when inheritanceModes is empty, Exomiser generates "empty" .genes.tsv, .variants.tsv and .vcf.gz files. Empty in the sense that the header rows exist but there is no variant/gene data. Curiously, the .html file still contains the expected content. To clarify, the expected content (for us) is what 13.0.0 produced.

This did not happen with version 13.0.0 and started happening with version 13.1.0. It also occurs on 13.2.0.

You can (hopefully) reproduce the issue as follows:

  1. Take any analysis .yml in the examples folder, e.g., NA19722_601952_AUTOSOMAL_RECESSIVE_POMP_13_29233225_5UTR_38 and comment out the content of inheritanceModes.
  2. Run Exomiser as usual (--analysis <the yml file>)
  3. Inspect the generated files (except .html) and notice the lack of data

We expected this usecase to be supported according to the comment on https://exomiser.readthedocs.io/en/latest/advanced_analysis.html#inheritancemodes, are we missing something?

Thanks for the work on Exomiser and Genomiser!

julesjacobsen commented 1 year ago

Hi! Sorry about the issue and thanks for an easily reproducible bug report! I hope you found a workaround to the issue (adding ANY: 2.0 to the inheritanceModes) whilst this was broken.

This will be fixed in the upcoming 13.2.1 release...