VEP GUI not returning LOFTEE output?
1
0
Entering edit mode
14 months ago
brismiller ▴ 40

Hey all,

I am using ensembl's VEP tool (http://grch37.ensembl.org/Homo_sapiens/Tools/VEP?db=core) and it is working properly but in the output there is no LOFTEE output.

The resulting vcf has the following header line:

##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID|MANE|TSL|APPRIS|SIFT|PolyPhen|AF|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE">

As you can see there are no "LoF|LoF_filter|LoF_flags|LoF_info" fields.

I have looked through the settings/ parameters on the website but there is no mention of how to add LOFTEE prediction annotations.

Am I just missing something obvious here?

Any insight would be helpful, thanks!

vep ensembl loftee • 774 views
ADD COMMENT
4
Entering edit mode
14 months ago
Ben_Ensembl ★ 1.7k

Hi,

The LOFTEE plugin is not available through the VEP web interface. However, you can use the standalone command line VEP tool: [1] http://www.ensembl.org/info/docs/tools/vep/script/index.html [2] https://github.com/konradjk/loftee

Importantly, different LOFTEE code+ files set are needed for GRCh37 vs GRCh38, which will be important to consider during installation.

Also, you could consider using the REST API, which also has the LOFTEE plugin: http://grch37.rest.ensembl.org/documentation/info/vep_region_get

Best wishes

Ben Ensembl Helpdesk

ADD COMMENT
1
Entering edit mode

Thanks for the quick reply and suggestions! Having you online to help answer these types of simple questions saves me and my coworkers a lot of time and energy, and it is much appreciated.

I will use one of the standalone tools.

ADD REPLY

Login before adding your answer.

Traffic: 1954 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6