{"action":"opened","issue":{"url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/39","repository_url":"https://api.github.com/repos/cancerit/cgpBattenberg","labels_url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/39/labels{/name}","comments_url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/39/comments","events_url":"https://api.github.com/repos/cancerit/cgpBattenberg/issues/39/events","html_url":"https://github.com/cancerit/cgpBattenberg/issues/39","id":178720550,"number":39,"title":"battenberg --> SPRUCE","user":{"login":"ramaniak","id":6088710,"avatar_url":"https://avatars.githubusercontent.com/u/6088710?v=3","gravatar_id":"","url":"https://api.github.com/users/ramaniak","html_url":"https://github.com/ramaniak","followers_url":"https://api.github.com/users/ramaniak/followers","following_url":"https://api.github.com/users/ramaniak/following{/other_user}","gists_url":"https://api.github.com/users/ramaniak/gists{/gist_id}","starred_url":"https://api.github.com/users/ramaniak/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ramaniak/subscriptions","organizations_url":"https://api.github.com/users/ramaniak/orgs","repos_url":"https://api.github.com/users/ramaniak/repos","events_url":"https://api.github.com/users/ramaniak/events{/privacy}","received_events_url":"https://api.github.com/users/ramaniak/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-09-22T21:06:50Z","updated_at":"2016-09-22T21:06:50Z","closed_at":null,"body":"Hello,\r\nThis not really an issue, more of a request for some clarification. \r\nI am using battenberg to create the copy number inputs necessary for executing spruce (https://github.com/raphael-group/spruce). I was in discussion with the spruce developer and he suggested I get in touch with @sdentro regarding this clarification. \r\n\r\nOne of the inputs to spruce requires copy number information the header format for which is below:\r\n```\r\n chr     startpos        endpos  BAF     pval    LogR    ntot    nMaj1_A nMin1_A frac1_A nMaj2_A nMin2_A frac2_A SDfrac_A        SDfrac_A_BS     frac1_A_0.025   frac1_A_0.975   frac1_A_corrected_for_purity   frac2_A_corrected_for_purity\r\n\r\n```\r\n\r\nThe subclones.txt output from running battenberg has pretty much the same format except for the following\r\n1. I am missing the final 2 columns (the fraction purity corrected). Would I be right in presuming this is obtained by multiplying the frac1_A and Frac2_A values by the  sample cellularity  value generated by the software? \r\n2. In my output, I have all of the columns above (minus the purity corrected cols) plus an additional set of columns for B, C, D, E, F as below\r\n\r\n```\r\nchr     startpos        endpos  BAF     pval    LogR    ntot    nMaj1_A nMin1_A frac1_A nMaj2_A nMin2_A frac2_A SDfrac_A        SDfrac_A_BS     frac1_A_0.025   frac1_A_0.975   nMaj1_B nMin1_B frac1_B nMaj2_B nMin2_B frac2_B SDfrac_B        SDfrac_B_BS     frac1_B_0.025   frac1_B_0.975   nMaj1_C nMin1_C frac1_C nMaj2_C nMin2_C frac2_C SDfrac_C        SDfrac_C_BS     frac1_C_0.025   frac1_C_0.975   nMaj1_D nMin1_D frac1_D nMaj2_D nMin2_D frac2_D SDfrac_D        SDfrac_D_BS     frac1_D_0.025   frac1_D_0.975   nMaj1_E nMin1_E frac1_E nMaj2_E nMin2_E frac2_E SDfrac_E        SDfrac_E_BS     frac1_E_0.025   frac1_E_0.975   nMaj1_F nMin1_F frac1_F nMaj2_F nMin2_F frac2_F SDfrac_F        SDfrac_F_BS     frac1_F_0.025   frac1_F_0.975\r\n```\r\nCould you please clarify how I interpret what A,B,C,D,E, and F ? \r\n\r\nThanks\r\nArun\r\n\r\n "}}
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