{"action":"created","issue":{"url":"https://api.github.com/repos/fritzsedlazeck/Sniffles/issues/74","repository_url":"https://api.github.com/repos/fritzsedlazeck/Sniffles","labels_url":"https://api.github.com/repos/fritzsedlazeck/Sniffles/issues/74/labels{/name}","comments_url":"https://api.github.com/repos/fritzsedlazeck/Sniffles/issues/74/comments","events_url":"https://api.github.com/repos/fritzsedlazeck/Sniffles/issues/74/events","html_url":"https://github.com/fritzsedlazeck/Sniffles/issues/74","id":321599688,"node_id":"MDU6SXNzdWUzMjE1OTk2ODg=","number":74,"title":"All Homozygous Variant , DV = 0","user":{"login":"npatel22526","id":16415435,"node_id":"MDQ6VXNlcjE2NDE1NDM1","avatar_url":"https://avatars0.githubusercontent.com/u/16415435?v=4","gravatar_id":"","url":"https://api.github.com/users/npatel22526","html_url":"https://github.com/npatel22526","followers_url":"https://api.github.com/users/npatel22526/followers","following_url":"https://api.github.com/users/npatel22526/following{/other_user}","gists_url":"https://api.github.com/users/npatel22526/gists{/gist_id}","starred_url":"https://api.github.com/users/npatel22526/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/npatel22526/subscriptions","organizations_url":"https://api.github.com/users/npatel22526/orgs","repos_url":"https://api.github.com/users/npatel22526/repos","events_url":"https://api.github.com/users/npatel22526/events{/privacy}","received_events_url":"https://api.github.com/users/npatel22526/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-05-09T14:43:27Z","updated_at":"2018-06-25T16:56:32Z","closed_at":null,"author_association":"NONE","body":"Hello, \r\n\r\nI have low coverage 10X Pacbio data , mapped using ngmlr. When I ran Snifflesv1.0.9 with the bam all the genotypes were homozygous. Also DV value is \"0\" for all variants in VCF\r\n\r\nHere is what i ran, \r\n`sniffles -m alignments.md.bam --vcf alignments.md.SV.vcf --min_support 2 --max_distance 600 --threads 16 -l 2 --genotype --cluster`\r\n\r\nOne more observation when I ran above command it output **del_ratio = -nan** and  **ins_ratio = inf**. I am not sure if I have to explicitly add the ratio thresholds for Parameter estimation. \r\n\r\nCan you comment on \"--min_zmw\" ,  what would be a reasonable cutoff for 10X coverage ?\r\n\r\nBest, \r\nNick\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/fritzsedlazeck/Sniffles/issues/comments/400022014","html_url":"https://github.com/fritzsedlazeck/Sniffles/issues/74#issuecomment-400022014","issue_url":"https://api.github.com/repos/fritzsedlazeck/Sniffles/issues/74","id":400022014,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMDAyMjAxNA==","user":{"login":"fritzsedlazeck","id":2081951,"node_id":"MDQ6VXNlcjIwODE5NTE=","avatar_url":"https://avatars0.githubusercontent.com/u/2081951?v=4","gravatar_id":"","url":"https://api.github.com/users/fritzsedlazeck","html_url":"https://github.com/fritzsedlazeck","followers_url":"https://api.github.com/users/fritzsedlazeck/followers","following_url":"https://api.github.com/users/fritzsedlazeck/following{/other_user}","gists_url":"https://api.github.com/users/fritzsedlazeck/gists{/gist_id}","starred_url":"https://api.github.com/users/fritzsedlazeck/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fritzsedlazeck/subscriptions","organizations_url":"https://api.github.com/users/fritzsedlazeck/orgs","repos_url":"https://api.github.com/users/fritzsedlazeck/repos","events_url":"https://api.github.com/users/fritzsedlazeck/events{/privacy}","received_events_url":"https://api.github.com/users/fritzsedlazeck/received_events","type":"User","site_admin":false},"created_at":"2018-06-25T16:56:32Z","updated_at":"2018-06-25T16:56:32Z","author_association":"OWNER","body":"Hey Nick,\r\nsorry for the delay. Is there a chance to share the bam file? We can also take that offline if you want: fritz.sedlazeck@gmail.com\r\n\r\nJust out of curiosity are these real Pacbio reads or simulated? I am just asking because I only see chr21 plus a few additional SV in the vcf file. \r\nthanks\r\nFritz "}}
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