GERP bigwig file location not concatenated properly

[dvg-p4]

I'm getting an error:

WARNING: Plugin 'LoF' went wrong: /home/dgealow/.vep/Pluginsgerp_conservation_scores.homo_sapiens.GRCh38.bw does not exist at /home/dgealow/.vep/Plugins/gerp_dist.pl line 72.

Note that it seems to be concatenating the slash-less filepath of the plugin directory I provided with the default expected filename, without a slash in-between. This issue seems to stem from:

https://github.com/konradjk/loftee/blob/a46b502a68c812c8ae0c5a5721c0603fe81cae8d/LoF.pm#L130

which I'm guessing should instead use catdir like the other path concatenations, something like this probably:

$self->{gerp_bigwig} = catdir($self->{loftee_path}, 'gerp_conservation_scores.homo_sapiens.GRCh38.bw') if !defined($self->{gerp_bigwig});

[jxcao98]

Have you solved this problem? I got the same error when using the GRCh37 version, but it worked fine in the GRCh38 version. Alternatively, could the LoF v1.0.4 be used directly for b37 vcf?

[jxcao98]

The master branch works fine for b37 vcf, while the latest version of LoF seems to not support GRCh37. This error will disappear if I use the correct version. What do you think?

[dvg-p4]

@jxcao98 This was a while ago, but I think I was able to just provide the loftee path with a trailing slash as a workaround:

vep --plugin LoF,loftee_path:/home/dgealow/.vep/Plugins/,[...]

[jxcao98]

Thank you for your reply!