{"action":"created","issue":{"url":"https://api.github.com/repos/vgteam/vg/issues/1975","repository_url":"https://api.github.com/repos/vgteam/vg","labels_url":"https://api.github.com/repos/vgteam/vg/issues/1975/labels{/name}","comments_url":"https://api.github.com/repos/vgteam/vg/issues/1975/comments","events_url":"https://api.github.com/repos/vgteam/vg/issues/1975/events","html_url":"https://github.com/vgteam/vg/issues/1975","id":377590282,"node_id":"MDU6SXNzdWUzNzc1OTAyODI=","number":1975,"title":"Potential false negative SV calls by (toil-)vg call","user":{"login":"eldariont","id":6477692,"node_id":"MDQ6VXNlcjY0Nzc2OTI=","avatar_url":"https://avatars0.githubusercontent.com/u/6477692?v=4","gravatar_id":"","url":"https://api.github.com/users/eldariont","html_url":"https://github.com/eldariont","followers_url":"https://api.github.com/users/eldariont/followers","following_url":"https://api.github.com/users/eldariont/following{/other_user}","gists_url":"https://api.github.com/users/eldariont/gists{/gist_id}","starred_url":"https://api.github.com/users/eldariont/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eldariont/subscriptions","organizations_url":"https://api.github.com/users/eldariont/orgs","repos_url":"https://api.github.com/users/eldariont/repos","events_url":"https://api.github.com/users/eldariont/events{/privacy}","received_events_url":"https://api.github.com/users/eldariont/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2018-11-05T21:29:01Z","updated_at":"2018-11-06T19:34:38Z","closed_at":null,"author_association":"CONTRIBUTOR","body":"Hi,\r\n\r\nfollowing up on today's call I open up this issue to discuss reasons for potential FN SVs in `vg call`. So this is what I did:\r\n\r\nI have 2 PacBio yeast assemblies: S288C and Y12. I aligned Y12 against S288C with nucmer and used Assemblytics to find SVs between the two. Then I used the resulting VCF to generate a vg graph with `vg construct`. Now I mapped Illumina reads from the same Y12 sample to the graph and ran `toil-vg call` to call SVs:\r\n```\r\ntoil-vg call --vg_docker quay.io/vgteam/vg:v1.11.0-74-gdab42acd-t242-run --nodeTypes c5.2xlarge:0.2,r4.large --minNodes 0,0 --maxNodes 1,1 --provisioner aws --batchSystem mesos --mesosMaster=${MASTER_IP}:5050 --metrics aws:us-west-2:vgcall-yeast-construct-jobstore $XG SRR4074383 aws:us-west-2:vgcall-yeast-construct-outstore --gams $GAM --recall --chroms chrI chrII chrIII chrIV chrV chrVI chrVII chrVIII chrIX chrX chrXI chrXII chrXIII chrXIV chrXV chrXVI 2> SRR4074383.construct.log\r\n```\r\n\r\nI now compared the resulting VCF file with the original VCF used to construct the graph and measured recall. I looked at the false negatives and noticed several examples where I don't understand why the variant wasn't at least called as heterozygous. I wouldn't be surprised if there were good reasons for not calling from the alignments but I don't understand `vg call` good enough to see these reasons yet.  Can anybody help?\r\n\r\nHere are 3 of the examples:\r\n\r\n**Example 1 (chrIII:148094, 104bp insertion)**\r\n![grafik](https://user-images.githubusercontent.com/6477692/48026844-0ed4af00-e0fc-11e8-8bcc-c15fb4eb64d2.png)\r\n\r\n**Example 2 (chrII: 197780, 333bp insertion)**\r\n![grafik](https://user-images.githubusercontent.com/6477692/48027132-c8cc1b00-e0fc-11e8-9ab5-079744e88c49.png)\r\n\r\n**Example 3 (chrXII: 9630121, 333bp insertion)**\r\n![grafik](https://user-images.githubusercontent.com/6477692/48027568-ff566580-e0fd-11e8-977f-ab571906a878.png)\r\n\r\nThe data can be found here:\r\n**graph**: /public/groups/cgl/users/daheller/yeast_graph/sequenceTubemapData/construct.vg\r\n**index**: /public/groups/cgl/users/daheller/yeast_graph/sequenceTubemapData/construct.vg.xg\r\n**alignments**: /public/groups/cgl/users/daheller/yeast_graph/sequenceTubemapData/SRR4074358.construct.subsample30.mapped.sorted.gam\r\n**alignment index**: /public/groups/cgl/users/daheller/yeast_graph/sequenceTubemapData/SRR4074358.construct.subsample30.mapped.sorted.gam.gai\r\n"},"comment":{"url":"https://api.github.com/repos/vgteam/vg/issues/comments/436380270","html_url":"https://github.com/vgteam/vg/issues/1975#issuecomment-436380270","issue_url":"https://api.github.com/repos/vgteam/vg/issues/1975","id":436380270,"node_id":"MDEyOklzc3VlQ29tbWVudDQzNjM4MDI3MA==","user":{"login":"eldariont","id":6477692,"node_id":"MDQ6VXNlcjY0Nzc2OTI=","avatar_url":"https://avatars0.githubusercontent.com/u/6477692?v=4","gravatar_id":"","url":"https://api.github.com/users/eldariont","html_url":"https://github.com/eldariont","followers_url":"https://api.github.com/users/eldariont/followers","following_url":"https://api.github.com/users/eldariont/following{/other_user}","gists_url":"https://api.github.com/users/eldariont/gists{/gist_id}","starred_url":"https://api.github.com/users/eldariont/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/eldariont/subscriptions","organizations_url":"https://api.github.com/users/eldariont/orgs","repos_url":"https://api.github.com/users/eldariont/repos","events_url":"https://api.github.com/users/eldariont/events{/privacy}","received_events_url":"https://api.github.com/users/eldariont/received_events","type":"User","site_admin":false},"created_at":"2018-11-06T19:34:38Z","updated_at":"2018-11-06T19:34:38Z","author_association":"CONTRIBUTOR","body":"Thanks Glenn for looking into this! That makes sense. I'm now recreating the graph with smaller nodes also because I was annoyed by these huge nodes myself ;-) Once that's done I will call again without the `-recall` option and will check how this changes the recall."}}
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