{"action":"opened","issue":{"url":"https://api.github.com/repos/ekg/freebayes/issues/500","repository_url":"https://api.github.com/repos/ekg/freebayes","labels_url":"https://api.github.com/repos/ekg/freebayes/issues/500/labels{/name}","comments_url":"https://api.github.com/repos/ekg/freebayes/issues/500/comments","events_url":"https://api.github.com/repos/ekg/freebayes/issues/500/events","html_url":"https://github.com/ekg/freebayes/issues/500","id":371525147,"node_id":"MDU6SXNzdWUzNzE1MjUxNDc=","number":500,"title":"Parallelize across cluster nodes for WGS","user":{"login":"marchoeppner","id":22975,"node_id":"MDQ6VXNlcjIyOTc1","avatar_url":"https://avatars2.githubusercontent.com/u/22975?v=4","gravatar_id":"","url":"https://api.github.com/users/marchoeppner","html_url":"https://github.com/marchoeppner","followers_url":"https://api.github.com/users/marchoeppner/followers","following_url":"https://api.github.com/users/marchoeppner/following{/other_user}","gists_url":"https://api.github.com/users/marchoeppner/gists{/gist_id}","starred_url":"https://api.github.com/users/marchoeppner/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/marchoeppner/subscriptions","organizations_url":"https://api.github.com/users/marchoeppner/orgs","repos_url":"https://api.github.com/users/marchoeppner/repos","events_url":"https://api.github.com/users/marchoeppner/events{/privacy}","received_events_url":"https://api.github.com/users/marchoeppner/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-10-18T13:15:59Z","updated_at":"2018-10-18T13:15:59Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI'd like to use Freebayes for calling variants across 200 genomes (30X PE). I understand there are several things I can do to parallelize this, but am unsure about possible restrictions here. \r\n\r\nI was planning on using intervals for calling, for example those distributed by the Broad Institute for their production pipeline (several hundred intervals of a few kb up to dozens of MB). I would partition these (per compute node), and pass them as <chr>:<start>-<stop> via STDIN to freebayes-parallel (custom script, I suppose). \r\n\r\nQuestions:\r\n\r\n1) Is there a number of snps or interval size I should have within a given process (a job on a node via freebayes-parallel) to make any of the internal processing work better? I.e. would Freebayes work for 200 genomes running in parallel of 1 interval of 1MB. Or does it require larger genomic regions for calling? At the very least, I should probably have several intervals per job, so that freebayes-parallel actually works on multiple CPUs, correct?\r\n\r\n2) Can i split contiguous intervals into smaller pieces for parallel processing, and if so, how does Freebayes deal with variants on the break points of these intervals? My concern is that Freebayes just takes a fairly long time to run on a 50MB interval across 200 genomes. So being able to split this into smaller bits would probably utilize our infrastructure a bit more efficiently. \r\n\r\nAny pointers would be greatly appreciated. \r\n\r\nCheers,\r\nMarc\r\n\r\n\r\n\r\n"}}
{"actor":{"display_login":"marchoeppner"}}