{"action":"created","issue":{"url":"https://api.github.com/repos/zstephens/neat-genreads/issues/36","repository_url":"https://api.github.com/repos/zstephens/neat-genreads","labels_url":"https://api.github.com/repos/zstephens/neat-genreads/issues/36/labels{/name}","comments_url":"https://api.github.com/repos/zstephens/neat-genreads/issues/36/comments","events_url":"https://api.github.com/repos/zstephens/neat-genreads/issues/36/events","html_url":"https://github.com/zstephens/neat-genreads/issues/36","id":306434486,"number":36,"title":"there is no AF  information in golden_vcf","user":{"login":"lituan","id":8915202,"avatar_url":"https://avatars2.githubusercontent.com/u/8915202?v=4","gravatar_id":"","url":"https://api.github.com/users/lituan","html_url":"https://github.com/lituan","followers_url":"https://api.github.com/users/lituan/followers","following_url":"https://api.github.com/users/lituan/following{/other_user}","gists_url":"https://api.github.com/users/lituan/gists{/gist_id}","starred_url":"https://api.github.com/users/lituan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lituan/subscriptions","organizations_url":"https://api.github.com/users/lituan/orgs","repos_url":"https://api.github.com/users/lituan/repos","events_url":"https://api.github.com/users/lituan/events{/privacy}","received_events_url":"https://api.github.com/users/lituan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-03-19T12:02:19Z","updated_at":"2018-04-26T17:02:12Z","closed_at":null,"author_association":"NONE","body":"Hi \r\n\r\nI download latest neat from this site and try to simulate some reads containing variants from a vcf, but the output vcf contains no AF information, here is the comman I use\r\n\r\npython neat-genreads-master/genReads.py -r human_g1k_v37.fasta -t test.bed -v test.vcf --bam --vcf -R 50 -o test --pe 300 30 -M 0.1 -p 10"},"comment":{"url":"https://api.github.com/repos/zstephens/neat-genreads/issues/comments/384715536","html_url":"https://github.com/zstephens/neat-genreads/issues/36#issuecomment-384715536","issue_url":"https://api.github.com/repos/zstephens/neat-genreads/issues/36","id":384715536,"user":{"login":"zstephens","id":8508373,"avatar_url":"https://avatars2.githubusercontent.com/u/8508373?v=4","gravatar_id":"","url":"https://api.github.com/users/zstephens","html_url":"https://github.com/zstephens","followers_url":"https://api.github.com/users/zstephens/followers","following_url":"https://api.github.com/users/zstephens/following{/other_user}","gists_url":"https://api.github.com/users/zstephens/gists{/gist_id}","starred_url":"https://api.github.com/users/zstephens/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/zstephens/subscriptions","organizations_url":"https://api.github.com/users/zstephens/orgs","repos_url":"https://api.github.com/users/zstephens/repos","events_url":"https://api.github.com/users/zstephens/events{/privacy}","received_events_url":"https://api.github.com/users/zstephens/received_events","type":"User","site_admin":false},"created_at":"2018-04-26T17:02:12Z","updated_at":"2018-04-26T17:02:12Z","author_association":"OWNER","body":"Because the random variants introduced by the simulator are in fact wholly random (i.e. not sourced from a database) it doesn't make sense to include population-level statistics like allele frequency. The WP field is meant to be a proxy to variant allele frequency (the expected proportion of reads at this site that you should expect to support the variant), and follows a similar format to standard GT values:\r\n\r\n(assuming you're simulating diploid genome:)\r\nhomozygous: WP=1/1\r\nheterozygous: WP=0/1 or WP=1/0\r\n\r\nIt makes sense that if an input vcf file had variants with AF fields, then I could push those forward into the output vcf created by NEAT. Is that what you're asking for? If you have downstream tools that are failing due to the lack of an AF field I would be open to adding an option to output dummy values for the random variants introduced via the -M input option. (e.g. AF=0.0 for randomly generated mutations)."}}
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