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Ensembl / VEP_plugins

Plugins for the Ensembl Variant Effect Predictor (VEP)
Apache License 2.0
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SpliceVault support for GRCh37 ? #751

Open yangyxt opened 1 week ago

yangyxt commented 1 week ago

Thank you for providing the TSV file for GRCh38 annotation, I wonder whether you could also include GRCh37.

If not available, could you please consider offering the script you use to convert the sql.gz file downloaded from https://storage.googleapis.com/misspl-db-data/misspl_events_300k_hg38.sql.gz to the tsv.gz file (link offered in the SpliceVault.pm file)

Much appreciated!

nakib103 commented 1 week ago

Hello @yangyxt ,

Thanks for your query!

For GRCh38, SpliceVault dev team provided us with the data. We will be getting in touch with them about getting the GRCh37 data for hosting. We will let you know once we get any update.

Best regards, Nakib

yangyxt commented 1 week ago

Hello @yangyxt ,

Thanks for your query!

For GRCh38, SpliceVault dev team provided us with the data. We will be getting in touch with them about getting the GRCh37 data for hosting. We will let you know once we get any update.

Best regards, Nakib

Dear Nakib,

Thank you for your reponse. During the waiting for your response, I wonder whether we can first try liftover the tsv file given the first several columns are chr, pos, ref, alt and all the other features are associated with the variants. The liftover might also include the coordinates of the splice site "chrx:xxxx".

Is this doable or meaningful ? Thanks!

nakib103 commented 1 week ago

Hi @yangyxt,

I would recommend getting in contact with SpliceVault team regarding this topic. If they recommend doing it and if so, if there is any preferred method/tool.

yangyxt commented 1 week ago

Sure, thanks. One more thing, do you happend to know how they generate the tabix index file ? Like which columns do they index on for the TSV file. Thanks!

Hi @yangyxt,

I would recommend getting in contact with SpliceVault team regarding this topic. If they recommend doing it and if so, if there is any preferred method/tool.

nakib103 commented 1 week ago

For the TSV file the --sequence is first column. --begin and --end both are the second column -

tabix -s 1 -b 2 -e 2 <tsv file>