LOFTEE doesnt actually annotate Loss-of-function variants

Question

[Qingyang Xiao]

Now I'm trying to use LOFTEE for loss-of-function variant annotation. Since LOFTEE is used in combination with VEP,

my command line is using the VEP example input:

./vep -i examples/homo_sapiens_GRCh37.vcf --cache -offline --force_overwrite --plugin LoF,loftee_path:loftee --dir_plugins loftee

I got the annotation by VEP indeed.

But the problem is that LOFTEE doesn't annotate at all. Some result instruction lines written like this were in the output files:

##LoF : Loss-of-function annotation (HC = High Confidence; LC = Low Confidence)
##LoF_filter : Reason for LoF not being HC
## LoF_flags : Possible warning flags for LoF
## LoF_info : Info used for LoF annotation

But the results actually doesn't contain these LOFTEE annotations.

Why?

[ATpoint]

Add added VEP and Ensembl tags to attract the Ensembl people.

[Ben_Ensembl]

Hi,

The LOFTEE plugin is not developed or maintained by Ensembl, so any issues you have running it should be raised with the author via their github page, https://github.com/konradjk/loftee

However, I noticed that a you are using the GRCh37 reference assembly. Please check you have installed / configured the plugin + plugin files correctly since different LOFTEE code+ files set are needed for GRCh37 vs GRCh38.

If you are still encountering issues, please send a sample of your input VCF to helpdesk[at]ensembl.org. Also, you could consider checking your input data using the REST API, which has the LOFTEE plugin: http://grch37.rest.ensembl.org/documentation/info/vep_region_get

Best wishes

Ben Ensembl Helpdesk