Plugin Conservation cannot annote GERP score for INDEL correctly

[jxcao98]

Plugin Conservation cannot annote GERP score for INDEL correctly

[jamie-m-a]

Hi @jxcao98

Yes you are understanding the intended functionality of the plugin correctly. I can reproduce the issue you have encountered and traced it back to the parsing of the scores from the bigwig file. I'll raise a ticket for this to be fixed in an upcoming release of Ensembl.

Meanwhile, you can use the following option of the plugin which takes data from the compara database rather than a bigwig file:

./vep -i variations.vcf --plugin Conservation,database,GERP_CONSERVATION_SCORE,mammals

I believe this method is working correctly to average the scores, though it will be noticeably slower than the file option.

[jxcao98]

Thanks for your quick reply!

I have another small suggestion. In our variant priorization pipeline, do we care more about the maximum value of all positions than the average? For example, for a long deletion, it deserves to be prioritized if it spans any of the conserved bases.

I‘d like to have an option that returns the maximum score for the region spanned by INDELs. Do you think this is worthwhile?

[jamie-m-a]

I agree Jixin - I think it makes perfect sense to have the most impactful reported as an option. I'll add that to bug fix.

[jxcao98]

Many thanks! I look forward to the new release!