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!