Funcotator 1.8 not working
Hi, I noticed a new data source for Funcotator, so I downloaded "funcotator_dataSources.v1.8.hg19.20230908s". However, when running I get the following error (using GATK v4.4.0.0 and Java v17.0.4): "java.lang.IllegalArgumentException: Unexpected value: Ensembl_canonical".
While setting up Funcotator its already gave a warning:
"09:45:00.982 WARN GencodeGtfCodec - GENCODE GTF Header line 1 has a version number that is above maximum tested version (v 34) (given: 43): ##description: evidence-based annotation of the human genome (GRCh38), version 43 (Ensembl 109), mapped to GRCh37 with gencode-backmap Continuing, but errors may occur."
I never had issues when running "funcotator_dataSources.v1.7.20200521s".
Any idea what is wrong, or I am doing wrong?
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Hi A. Brink
The resource file version 1.8 was created and updated for by changes introduced in GATK 4.5.0.0 which will be released soon therefore the error message also indicates the incompatibility of the version 1.8 and current GATK 4.4.0.0. If you still wish to use the newest resource you may try building GATK from the master branch of github repository or you may use the nightly docker builds of GATK both of which already includes funcotator updates for the resource bundle 1.8. Beware that this version is still being tested and although our team has tested it quite rigorously there may be edge cases uncaught and if you see any such error please let us know from here or open an issue in the github issues page so that it can be addressed quickly until GATK 4.5.0.0 release.
I hope this helps.
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