{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/817","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/817/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/817/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/817/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/817","id":67191393,"number":817,"title":"Support GRCh38","user":{"login":"schelhorn","id":5024959,"avatar_url":"https://avatars.githubusercontent.com/u/5024959?v=3","gravatar_id":"","url":"https://api.github.com/users/schelhorn","html_url":"https://github.com/schelhorn","followers_url":"https://api.github.com/users/schelhorn/followers","following_url":"https://api.github.com/users/schelhorn/following{/other_user}","gists_url":"https://api.github.com/users/schelhorn/gists{/gist_id}","starred_url":"https://api.github.com/users/schelhorn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/schelhorn/subscriptions","organizations_url":"https://api.github.com/users/schelhorn/orgs","repos_url":"https://api.github.com/users/schelhorn/repos","events_url":"https://api.github.com/users/schelhorn/events{/privacy}","received_events_url":"https://api.github.com/users/schelhorn/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":10,"created_at":"2015-04-08T18:35:43Z","updated_at":"2015-04-21T10:48:41Z","closed_at":null,"body":"I was wondering if there are any plans to support GRCh38 as an additional assembly. The alternate loci and decoy sequences are likely to improve both variant calling and expression studies. I suppose that the availability of genomes and annotations are not much of a problem anymore, but not all tools may be compatible. Could someone detail the major roadblocks concerning this issue? Thanks. "},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/94742658","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/817#issuecomment-94742658","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/817","id":94742658,"user":{"login":"chapmanb","id":39391,"avatar_url":"https://avatars.githubusercontent.com/u/39391?v=3","gravatar_id":"","url":"https://api.github.com/users/chapmanb","html_url":"https://github.com/chapmanb","followers_url":"https://api.github.com/users/chapmanb/followers","following_url":"https://api.github.com/users/chapmanb/following{/other_user}","gists_url":"https://api.github.com/users/chapmanb/gists{/gist_id}","starred_url":"https://api.github.com/users/chapmanb/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/chapmanb/subscriptions","organizations_url":"https://api.github.com/users/chapmanb/orgs","repos_url":"https://api.github.com/users/chapmanb/repos","events_url":"https://api.github.com/users/chapmanb/events{/privacy}","received_events_url":"https://api.github.com/users/chapmanb/received_events","type":"User","site_admin":false},"created_at":"2015-04-21T10:48:41Z","updated_at":"2015-04-21T10:48:41Z","body":"Alison and Mick -- thanks so much for investigating the CrossMap approach. Those numbers looks great, I'd be happy to include the GATK supporting files into bcbio so we have them available. We can always iterate and update as we continue to evaluate these.\r\n\r\nPractically, I added in downloads of hg38/GRCh38 (without alternative sequences) to bcbio. If you update to the latest version of the development code you can do:\r\n```\r\nbcbio_nextgen.py upgrade -u development\r\nbcbio_nextgen.py upgrade --data --genomes hg38-noalt\r\n```\r\nand it will install the reference genome, bwa/bowtie2 indices, and dbSNP 142. The references and indices all come from NCBI:\r\n\r\nftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38/seqs_for_alignment_pipelines/README_ANALYSIS_SETS\r\n\r\nI haven't done any runs with the hg38 genome but having the basic data installation in place is step one.\r\n\r\nAaron, on the logistics side I used your GGD approach to manage the installation. The separation between the download/prep code and the machinery to actually do the installations is nice -- it makes the data provenance clear. I needed to stray from your initial GGD implementation of streaming the results of one download to one file since these preps involved picking and prepping multiple files from the initial tarballs. I implemented a take on GGD which uses a temporary directory, runs all of the file prep commands as a bash script, then pulls out the final files into the output directory when updated:\r\n\r\nhttps://github.com/chapmanb/cloudbiolinux/tree/master/ggd-recipes\r\nhttps://github.com/chapmanb/cloudbiolinux/blob/master/cloudbio/biodata/ggd.py\r\n\r\nI'd love to try and coordinate this with what you want to do for GEMINI so we can have a single approach to get one set of downloaded data.\r\n\r\nThanks all for the discussion and ideas."}}