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docs (parseVEP): clarify that the default VEP output is TSV
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zhuchcn committed Oct 16, 2024
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Expand Up @@ -29,7 +29,7 @@ moPepGen relies on Ensembl Variant Effect Predictor ([VEP](https://www.ensembl.o

Please refer to the official [VEP Tutorial](https://www.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html) for instructions on downloading, installing and running VEP. The key is to ensure that the annotation version used in `VEP` is the same as the one you would like to use with moPepGen.

`parseVEP` currently only supports the TSV output of `VEP`, please set the suffix of `--output_file` to `.tsv` to ensure the correct format is outputted by `VEP`.
`parseVEP` currently only supports the TSV output of `VEP`, please set the suffix of `--output_file` to `.tsv` to ensure the correct format is outputted by `VEP`. `VEP`'s default output format is tab-delimited, and the `--tab` option adds extra columns to the output that are not used by moPepGen. So including or excluding `--tab` will not impact the results of moPepGen.

### Using an Ensembl GTF

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