{"action":"opened","issue":{"url":"https://api.github.com/repos/atks/vt/issues/14","labels_url":"https://api.github.com/repos/atks/vt/issues/14/labels{/name}","comments_url":"https://api.github.com/repos/atks/vt/issues/14/comments","events_url":"https://api.github.com/repos/atks/vt/issues/14/events","html_url":"https://github.com/atks/vt/issues/14","id":62713184,"number":14,"title":"vt cat results in chrom replacement","user":{"login":"cboustred","id":3475795,"avatar_url":"https://avatars.githubusercontent.com/u/3475795?v=3","gravatar_id":"","url":"https://api.github.com/users/cboustred","html_url":"https://github.com/cboustred","followers_url":"https://api.github.com/users/cboustred/followers","following_url":"https://api.github.com/users/cboustred/following{/other_user}","gists_url":"https://api.github.com/users/cboustred/gists{/gist_id}","starred_url":"https://api.github.com/users/cboustred/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cboustred/subscriptions","organizations_url":"https://api.github.com/users/cboustred/orgs","repos_url":"https://api.github.com/users/cboustred/repos","events_url":"https://api.github.com/users/cboustred/events{/privacy}","received_events_url":"https://api.github.com/users/cboustred/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-03-18T14:52:28Z","updated_at":"2015-03-18T14:52:28Z","closed_at":null,"body":"Hi,\r\n\r\nThanks for developing vt - looks like it could be really helpful\r\n\r\nI've come across an issue when using vt cat to combine VCF files generated on the same set of samples but on different chromosomes (as per the example in the docs: http://genome.sph.umich.edu/wiki/Vt#Concatenate). The chromosome name is being replaced with whatever it is in the first VCF file supplied. I've tried with both specifying the VCFs in full or using an input file list (-L)\r\n\r\nAn example of what I'm trying to do:\r\n\r\nvt cat chr1.vcf chr2.vcf -o cat.vcf\r\n\r\nThe variants are concatenated in cat.vcf, however all the chromosome names would be converted to chr1 \r\n\r\nBW\r\n\r\nChris\r\n\r\n"}}