{"action":"closed","issue":{"url":"https://api.github.com/repos/mskcc/vcf2maf/issues/167","repository_url":"https://api.github.com/repos/mskcc/vcf2maf","labels_url":"https://api.github.com/repos/mskcc/vcf2maf/issues/167/labels{/name}","comments_url":"https://api.github.com/repos/mskcc/vcf2maf/issues/167/comments","events_url":"https://api.github.com/repos/mskcc/vcf2maf/issues/167/events","html_url":"https://github.com/mskcc/vcf2maf/issues/167","id":321974795,"node_id":"MDU6SXNzdWUzMjE5NzQ3OTU=","number":167,"title":"--retain-info missing data in MAF file","user":{"login":"bibbers93","id":32960596,"node_id":"MDQ6VXNlcjMyOTYwNTk2","avatar_url":"https://avatars2.githubusercontent.com/u/32960596?v=4","gravatar_id":"","url":"https://api.github.com/users/bibbers93","html_url":"https://github.com/bibbers93","followers_url":"https://api.github.com/users/bibbers93/followers","following_url":"https://api.github.com/users/bibbers93/following{/other_user}","gists_url":"https://api.github.com/users/bibbers93/gists{/gist_id}","starred_url":"https://api.github.com/users/bibbers93/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bibbers93/subscriptions","organizations_url":"https://api.github.com/users/bibbers93/orgs","repos_url":"https://api.github.com/users/bibbers93/repos","events_url":"https://api.github.com/users/bibbers93/events{/privacy}","received_events_url":"https://api.github.com/users/bibbers93/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":{"login":"ckandoth","id":516941,"node_id":"MDQ6VXNlcjUxNjk0MQ==","avatar_url":"https://avatars2.githubusercontent.com/u/516941?v=4","gravatar_id":"","url":"https://api.github.com/users/ckandoth","html_url":"https://github.com/ckandoth","followers_url":"https://api.github.com/users/ckandoth/followers","following_url":"https://api.github.com/users/ckandoth/following{/other_user}","gists_url":"https://api.github.com/users/ckandoth/gists{/gist_id}","starred_url":"https://api.github.com/users/ckandoth/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ckandoth/subscriptions","organizations_url":"https://api.github.com/users/ckandoth/orgs","repos_url":"https://api.github.com/users/ckandoth/repos","events_url":"https://api.github.com/users/ckandoth/events{/privacy}","received_events_url":"https://api.github.com/users/ckandoth/received_events","type":"User","site_admin":false},"assignees":[{"login":"ckandoth","id":516941,"node_id":"MDQ6VXNlcjUxNjk0MQ==","avatar_url":"https://avatars2.githubusercontent.com/u/516941?v=4","gravatar_id":"","url":"https://api.github.com/users/ckandoth","html_url":"https://github.com/ckandoth","followers_url":"https://api.github.com/users/ckandoth/followers","following_url":"https://api.github.com/users/ckandoth/following{/other_user}","gists_url":"https://api.github.com/users/ckandoth/gists{/gist_id}","starred_url":"https://api.github.com/users/ckandoth/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ckandoth/subscriptions","organizations_url":"https://api.github.com/users/ckandoth/orgs","repos_url":"https://api.github.com/users/ckandoth/repos","events_url":"https://api.github.com/users/ckandoth/events{/privacy}","received_events_url":"https://api.github.com/users/ckandoth/received_events","type":"User","site_admin":false}],"milestone":null,"comments":9,"created_at":"2018-05-10T15:30:05Z","updated_at":"2018-10-04T14:57:45Z","closed_at":"2018-10-04T14:57:45Z","author_association":"NONE","body":"Hi, I am using the following command\r\n\r\n``` \r\nvcf2maf.pl --input-vcf no_chr.vcf --output-maf test.maf --tumor-id Sample1 --ref-fasta ~/.vep/homo_sapiens/91_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --retain-info GT,GQ,SDP,DP,RD,AD,FREQ,PVAL,RBQ,ABQ,RDF,RDR,ADF,AD\r\n\r\n```\r\nto generate a maf file from a vcf file. The outputted maf file has columns GT GQ SDP etc. but there is no data from the vcf file in these columns.\r\n\r\n"}}
{"actor":{"display_login":"ckandoth"}}