{"action":"closed","issue":{"url":"https://api.github.com/repos/rmcolq/pandora/issues/101","repository_url":"https://api.github.com/repos/rmcolq/pandora","labels_url":"https://api.github.com/repos/rmcolq/pandora/issues/101/labels{/name}","comments_url":"https://api.github.com/repos/rmcolq/pandora/issues/101/comments","events_url":"https://api.github.com/repos/rmcolq/pandora/issues/101/events","html_url":"https://github.com/rmcolq/pandora/issues/101","id":378751953,"node_id":"MDU6SXNzdWUzNzg3NTE5NTM=","number":101,"title":"Want a genotyped Multisample VCF","user":{"login":"rmcolq","id":9866043,"node_id":"MDQ6VXNlcjk4NjYwNDM=","avatar_url":"https://avatars1.githubusercontent.com/u/9866043?v=4","gravatar_id":"","url":"https://api.github.com/users/rmcolq","html_url":"https://github.com/rmcolq","followers_url":"https://api.github.com/users/rmcolq/followers","following_url":"https://api.github.com/users/rmcolq/following{/other_user}","gists_url":"https://api.github.com/users/rmcolq/gists{/gist_id}","starred_url":"https://api.github.com/users/rmcolq/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rmcolq/subscriptions","organizations_url":"https://api.github.com/users/rmcolq/orgs","repos_url":"https://api.github.com/users/rmcolq/repos","events_url":"https://api.github.com/users/rmcolq/events{/privacy}","received_events_url":"https://api.github.com/users/rmcolq/received_events","type":"User","site_admin":false},"labels":[{"id":1091548254,"node_id":"MDU6TGFiZWwxMDkxNTQ4MjU0","url":"https://api.github.com/repos/rmcolq/pandora/labels/paper","name":"paper","color":"38f4af","default":false},{"id":1091548127,"node_id":"MDU6TGFiZWwxMDkxNTQ4MTI3","url":"https://api.github.com/repos/rmcolq/pandora/labels/thesis","name":"thesis","color":"e9f287","default":false}],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-11-08T14:20:38Z","updated_at":"2018-11-29T11:19:01Z","closed_at":"2018-11-29T11:19:01Z","author_association":"OWNER","body":"On line https://github.com/rmcolq/pandora/blob/bed2a41f7d9aab36f2b9322852e5ef934a7ee85b/src/compare_main.cpp#L320 in `pandora compare` we run the `genotype` command. An example VCF from a previous `compare` run \r\n`/nfs/leia/research/iqbal/rff/data/pandora/compare_cmd_test/outdir/GC00000002_17/GC00000002_17.multisample.vcf`\r\ndoes not have coverage information and hence running the genotype command did not do anything (genotype skips if can't do anything). For comparison, a VCF output from the `pandora map` command looks like this \r\n`/nfs/leia/research/iqbal/rmcolq/projects/pandora_variation/analysis/cardio_H131800734/genotyping/pandora_genotyped_30X.vcf` and has the coverage information, and so the genotype information.\r\n\r\nThe coverage information should I think be added  on line https://github.com/rmcolq/pandora/blob/bed2a41f7d9aab36f2b9322852e5ef934a7ee85b/src/compare_main.cpp#L285 which calls this function here https://github.com/rmcolq/pandora/blob/bed2a41f7d9aab36f2b9322852e5ef934a7ee85b/src/localPRG.cpp#L1409\r\n\r\nFor this to work, there need to be coverages in the kmergraph associated with the pannode.\r\n"}}
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