table gerp_exons

[hliang]

LOFTEE fails and gives empty fields in the output. Error msg:

DBD::SQLite::db prepare failed: no such table: gerp_exons at /path/to/vep/ensembl-vep-94.5-0/gerp_dist.pl line 129, <__ANONIO__> line 117945.
WARNING: Plugin 'LoF' went wrong: Can't call method "execute" on an undefined value at /path/to/vep/ensembl-vep-94.5-0/gerp_dist.pl line 130, <__ANONIO__> line 117945.

Looks like it's looking for gerp_exons table. Where may I get a copy of that file? https://github.com/konradjk/loftee/blob/df3d29e137c71655b708c1b98bd5d0a127d8802f/gerp_dist.pl#L129

[rvernica]

I'm running into this as well. Any hints on how to get this table would be appreciated.

[hliang]

I get around this issue by using an earlier version v0.3-beta ( 6a99f18ae1c69a2306e2fc46f1586653b301ab8c), which doesn't require gerp_exons.

[rvernica]

Thanks, yes the older version does not seem to require that table.

For GRCh37, I found the gerp_exons table in the phylocsf_gerp.sql file from here:

> sqlite3 phylocsf_gerp.sql
sqlite> .tables
gerp_exons     phylocsf_data