{"action":"opened","issue":{"url":"https://api.github.com/repos/BD2KGenomics/brca/issues/36","labels_url":"https://api.github.com/repos/BD2KGenomics/brca/issues/36/labels{/name}","comments_url":"https://api.github.com/repos/BD2KGenomics/brca/issues/36/comments","events_url":"https://api.github.com/repos/BD2KGenomics/brca/issues/36/events","html_url":"https://github.com/BD2KGenomics/brca/issues/36","id":86333296,"number":36,"title":"Produce sample data to verify that we are following VCF rules regarding indels","user":{"login":"melissacline","id":1714823,"avatar_url":"https://avatars.githubusercontent.com/u/1714823?v=3","gravatar_id":"","url":"https://api.github.com/users/melissacline","html_url":"https://github.com/melissacline","followers_url":"https://api.github.com/users/melissacline/followers","following_url":"https://api.github.com/users/melissacline/following{/other_user}","gists_url":"https://api.github.com/users/melissacline/gists{/gist_id}","starred_url":"https://api.github.com/users/melissacline/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/melissacline/subscriptions","organizations_url":"https://api.github.com/users/melissacline/orgs","repos_url":"https://api.github.com/users/melissacline/repos","events_url":"https://api.github.com/users/melissacline/events{/privacy}","received_events_url":"https://api.github.com/users/melissacline/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-06-08T21:13:38Z","updated_at":"2015-06-08T21:13:38Z","closed_at":null,"body":"From Max:\n\nFor indels in homopolymers, VCF places the indel on the first base of the stretch, whereas HGVS uses the last base (e.g. AAA with an A insertion gets written position=1 in VCF and position=3 in HGVS).\n\nWe know that some databases clearly use VCF natively (1000 Genomes, Exac), others clearly use HGVS (LOVD) and some might have a rule that we are not aware of yet (NCBI BIC). We should be sure we're doing these conversions in the right way, i.e. everything to VCF rules. In addition, we convert from HGVS to VCF with the Counsyl converter (pyhgvs) which might introduce additional errors.\n\nMolly, can you write out the differing rows to a text file, one for each combination of databases? In that way we can look over the differences. I'm especially curious about the differences between Exac and 1000 Genomes. As far as I know Exac imported (=copied) the 1000 genomes data."}}