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!
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written
by
brismiller •
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
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.
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