{"action":"created","issue":{"url":"https://api.github.com/repos/churchill-lab/g2gtools/issues/13","repository_url":"https://api.github.com/repos/churchill-lab/g2gtools","labels_url":"https://api.github.com/repos/churchill-lab/g2gtools/issues/13/labels{/name}","comments_url":"https://api.github.com/repos/churchill-lab/g2gtools/issues/13/comments","events_url":"https://api.github.com/repos/churchill-lab/g2gtools/issues/13/events","html_url":"https://github.com/churchill-lab/g2gtools/issues/13","id":354776435,"node_id":"MDU6SXNzdWUzNTQ3NzY0MzU=","number":13,"title":"Unable to Generate Correct *.chain file for Inbred Mouse Strains","user":{"login":"rantingswede373","id":18125936,"node_id":"MDQ6VXNlcjE4MTI1OTM2","avatar_url":"https://avatars3.githubusercontent.com/u/18125936?v=4","gravatar_id":"","url":"https://api.github.com/users/rantingswede373","html_url":"https://github.com/rantingswede373","followers_url":"https://api.github.com/users/rantingswede373/followers","following_url":"https://api.github.com/users/rantingswede373/following{/other_user}","gists_url":"https://api.github.com/users/rantingswede373/gists{/gist_id}","starred_url":"https://api.github.com/users/rantingswede373/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/rantingswede373/subscriptions","organizations_url":"https://api.github.com/users/rantingswede373/orgs","repos_url":"https://api.github.com/users/rantingswede373/repos","events_url":"https://api.github.com/users/rantingswede373/events{/privacy}","received_events_url":"https://api.github.com/users/rantingswede373/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2018-08-28T15:09:57Z","updated_at":"2018-08-28T15:39:18Z","closed_at":"2018-08-28T15:39:09Z","author_association":"NONE","body":"I'm attempting to use g2gtools to convert coordinates between two inbred mouse strains (C57Bl/6J and CAST/EiJ) following the documentation online. If I ignore Indels it seems to work fine with the patched genome reflecting known variants in a few quick spot checks. The generation of the chain file for coordinate conversion does not seem to be working however, as the file is very small and a test run with a signal bed file returns the same coordinates as in the original reference despite there being millions of Indel variants between the two.\r\n\r\nI'm using version 0.1.3 with the relevant command being:\r\ng2gtools vcf2chain --pass -f NCBIM37_um.fa -i mgp.v2.indels.annot.reformat.vcf.gz -s CASTEiJ -o mm9-to-CASTEiJ.chain\r\n\r\nThis returns a stdout as below:\r\n`Chromosome: 1\r\nSTATISTICS\r\nChromosome: 10\r\nSTATISTICS\r\nChromosome: 11\r\nSTATISTICS\r\n...\r\n...\r\ncomplete\r\nParsed 0 total lines\r\nChain file created\r\nExecution complete: 00:00:10.13\r\n`\r\n\r\nSo obviously something is off, although no explicit error messages come up. I confirmed that the strain is indeed \"CASTEiJ\" and not \"CAST_EiJ\" or some other variant as well as any other small issues that may have led to this. I'd like to try version 0.2.0, but haven't been able to successfully install it. Any help would be greatly appreciated!"},"comment":{"url":"https://api.github.com/repos/churchill-lab/g2gtools/issues/comments/416634814","html_url":"https://github.com/churchill-lab/g2gtools/issues/13#issuecomment-416634814","issue_url":"https://api.github.com/repos/churchill-lab/g2gtools/issues/13","id":416634814,"node_id":"MDEyOklzc3VlQ29tbWVudDQxNjYzNDgxNA==","user":{"login":"kbchoi-jax","id":7860891,"node_id":"MDQ6VXNlcjc4NjA4OTE=","avatar_url":"https://avatars1.githubusercontent.com/u/7860891?v=4","gravatar_id":"","url":"https://api.github.com/users/kbchoi-jax","html_url":"https://github.com/kbchoi-jax","followers_url":"https://api.github.com/users/kbchoi-jax/followers","following_url":"https://api.github.com/users/kbchoi-jax/following{/other_user}","gists_url":"https://api.github.com/users/kbchoi-jax/gists{/gist_id}","starred_url":"https://api.github.com/users/kbchoi-jax/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/kbchoi-jax/subscriptions","organizations_url":"https://api.github.com/users/kbchoi-jax/orgs","repos_url":"https://api.github.com/users/kbchoi-jax/repos","events_url":"https://api.github.com/users/kbchoi-jax/events{/privacy}","received_events_url":"https://api.github.com/users/kbchoi-jax/received_events","type":"User","site_admin":false},"created_at":"2018-08-28T15:39:18Z","updated_at":"2018-08-28T15:39:18Z","author_association":"MEMBER","body":"Sorry I never tested `g2gtools` with those old versions. I note they released REL-1807 recently."}}
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