{"issue":{"state":"closed","created_at":"2011-12-14T01:56:44Z","updated_at":"2011-12-15T02:35:28Z","user":{"gravatar_id":"907db62471c84437d0875095402e94b6","id":39391,"url":"https://api.github.com/users/chapmanb","login":"chapmanb","avatar_url":"https://secure.gravatar.com/avatar/907db62471c84437d0875095402e94b6?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png"},"comments":2,"body":"Freebayes will ouput variant calls that have the same base as the reference sequence:\r\n\r\n    #CHROM  POS     ID      REF     ALT     QUAL    FILTER\r\n    5       165062085       .       G       G       82.086  .  \r\n\r\nThese cause GATK variant manipulation tools to raise an error when working downstream with Freebayes calls, which identified the issue.\r\n\r\nHere is a BAM file with 2 reads that reproduces the problem, using the Broad GRCh37 genome:\r\n\r\nhttps://s3.amazonaws.com/chapmanb/freebayes_nochange_call.bam\r\nftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/1.2/b37/human_g1k_v37.fasta.gz\r\n\r\n    freebayes -b freebayes_nochange_call.bam -v test_nochange.vcf -f  GRCh37.fa\r\n\r\nPlease let me know if any other information would be helpful.","assignee":null,"id":2546824,"labels":[],"pull_request":{"patch_url":null,"html_url":null,"diff_url":null},"number":24,"title":"Called variants with same base as reference sequence","html_url":"https://github.com/ekg/freebayes/issues/24","closed_at":"2011-12-15T02:35:28Z","milestone":null,"url":"https://api.github.com/repos/ekg/freebayes/issues/24"},"action":"created","comment":{"created_at":"2011-12-15T02:35:28Z","updated_at":"2011-12-15T02:35:28Z","user":{"gravatar_id":"907db62471c84437d0875095402e94b6","id":39391,"url":"https://api.github.com/users/chapmanb","login":"chapmanb","avatar_url":"https://secure.gravatar.com/avatar/907db62471c84437d0875095402e94b6?d=https://a248.e.akamai.net/assets.github.com%2Fimages%2Fgravatars%2Fgravatar-140.png"},"body":"Eric;\r\nThat works perfect; no more non-changing bases. Thanks for looking at this so quickly; much appreciated.","id":3155869,"url":"https://api.github.com/repos/ekg/freebayes/issues/comments/3155869"}}