{"action":"created","issue":{"url":"https://api.github.com/repos/Clinical-Genomics/scout/issues/894","repository_url":"https://api.github.com/repos/Clinical-Genomics/scout","labels_url":"https://api.github.com/repos/Clinical-Genomics/scout/issues/894/labels{/name}","comments_url":"https://api.github.com/repos/Clinical-Genomics/scout/issues/894/comments","events_url":"https://api.github.com/repos/Clinical-Genomics/scout/issues/894/events","html_url":"https://github.com/Clinical-Genomics/scout/issues/894","id":339497244,"node_id":"MDU6SXNzdWUzMzk0OTcyNDQ=","number":894,"title":"scout v4 cannot parse vep92 annotations.","user":{"login":"nvteja","id":16638984,"node_id":"MDQ6VXNlcjE2NjM4OTg0","avatar_url":"https://avatars1.githubusercontent.com/u/16638984?v=4","gravatar_id":"","url":"https://api.github.com/users/nvteja","html_url":"https://github.com/nvteja","followers_url":"https://api.github.com/users/nvteja/followers","following_url":"https://api.github.com/users/nvteja/following{/other_user}","gists_url":"https://api.github.com/users/nvteja/gists{/gist_id}","starred_url":"https://api.github.com/users/nvteja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nvteja/subscriptions","organizations_url":"https://api.github.com/users/nvteja/orgs","repos_url":"https://api.github.com/users/nvteja/repos","events_url":"https://api.github.com/users/nvteja/events{/privacy}","received_events_url":"https://api.github.com/users/nvteja/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-07-09T15:25:21Z","updated_at":"2018-07-11T15:03:14Z","closed_at":"2018-07-10T17:54:31Z","author_association":"NONE","body":"Hello,\r\nI cannot get scout v4 to parse vep92 annotations specifically CADD_Phred, gnomAD frequencies. Here is my vep92 header.\r\n\r\n##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|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|REFSEQ_MATCH|SOURCE|GIVEN_REF|USED_REF|BAM_EDIT|GENE_PHENO|SIFT|PolyPhen|DOMAINS|miRNA|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|CADD_phred|FATHMM_pred|MetaSVM_pred|MutationTaster_pred|Polyphen2_HVAR_pred|SIFT_pred\">\r\n\r\nwhen I manually replace CADD_Phred with CADD_PHRED (just capitalize the word Phred), scout is able to load CADD properly. Also, regardless of the capitalization, I could not get gnomAD frequencies to load at all. Is this a bug or am I missing something fundamental in the way the vcf should be formatted for scout?\r\n\r\nThank you,\r\nTeja."},"comment":{"url":"https://api.github.com/repos/Clinical-Genomics/scout/issues/comments/404202554","html_url":"https://github.com/Clinical-Genomics/scout/issues/894#issuecomment-404202554","issue_url":"https://api.github.com/repos/Clinical-Genomics/scout/issues/894","id":404202554,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNDIwMjU1NA==","user":{"login":"nvteja","id":16638984,"node_id":"MDQ6VXNlcjE2NjM4OTg0","avatar_url":"https://avatars1.githubusercontent.com/u/16638984?v=4","gravatar_id":"","url":"https://api.github.com/users/nvteja","html_url":"https://github.com/nvteja","followers_url":"https://api.github.com/users/nvteja/followers","following_url":"https://api.github.com/users/nvteja/following{/other_user}","gists_url":"https://api.github.com/users/nvteja/gists{/gist_id}","starred_url":"https://api.github.com/users/nvteja/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nvteja/subscriptions","organizations_url":"https://api.github.com/users/nvteja/orgs","repos_url":"https://api.github.com/users/nvteja/repos","events_url":"https://api.github.com/users/nvteja/events{/privacy}","received_events_url":"https://api.github.com/users/nvteja/received_events","type":"User","site_admin":false},"created_at":"2018-07-11T15:03:14Z","updated_at":"2018-07-11T15:03:14Z","author_association":"NONE","body":"Hello Måns,\r\n\r\nLooks like Scout still isnt parsing/recognizing  gnomad_AF column from the VEP header. I can see CADD_Phred and 1000G frequencies however. Could you please look into it?\r\n\r\nThank you,\r\nTeja"}}
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