VEP GUI not returning LOFTEE output?
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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
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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

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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.