| Previous changeset 3:c758125c56d8 (2015-05-25) Next changeset 5:ed0dbb61f0e1 (2016-08-04) |
|
Commit message:
planemo upload |
|
modified:
kggseq_variant_selection.xml tool_dependencies.xml |
|
added:
examples/assoc.hg19.vcf.gz examples/assoc.hg19.vcf.gz.tbi.gz examples/assoc.ped examples/geneset.txt examples/hg19_breast.txt examples/param.rare.disease.hg19.txt examples/rare.disease.hg19.vcf examples/rare.disease.ped.txt righe_tolte.txt |
|
removed:
COPYING |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c COPYING --- a/COPYING Mon May 25 18:01:25 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,23 +0,0 @@ -Copyright © 2013-2015 CRS4 Srl. http://www.crs4.it/ -Created by: -Paolo Uva <paolo.uva@crs4.it> -Nicola Soranzo <nicola.soranzo@tgac.ac.uk> - -Permission is hereby granted, free of charge, to any person obtaining a -copy of this software and associated documentation files (the -"Software"), to deal in the Software without restriction, including -without limitation the rights to use, copy, modify, merge, publish, -distribute, sublicense, and/or sell copies of the Software, and to -permit persons to whom the Software is furnished to do so, subject to -the following conditions: - -The above copyright notice and this permission notice shall be included -in all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS -OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. -IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY -CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, -TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE -SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c examples/assoc.hg19.vcf.gz |
| b |
| Binary file examples/assoc.hg19.vcf.gz has changed |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c examples/assoc.hg19.vcf.gz.tbi.gz |
| b |
| Binary file examples/assoc.hg19.vcf.gz.tbi.gz has changed |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c examples/assoc.ped --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/assoc.ped Thu Aug 04 04:40:06 2016 -0400 |
| b |
| b'@@ -0,0 +1,984 @@\n+fid\tiid\tfatid\tmatid\tsex\tdisease1\tage\n+HG01583\tHG01583\t0\t0\t1\t1\t74\n+HG01586\tHG01586\t0\t0\t1\t1\t40\n+HG01589\tHG01589\t0\t0\t1\t1\t58\n+HG01593\tHG01593\t0\t0\t1\t1\t65\n+HG02490\tHG02490\t0\t0\t2\t1\t9\n+HG02491\tHG02491\t0\t0\t2\t1\t69\n+HG02493\tHG02493\t0\t0\t1\t1\t11\n+HG02494\tHG02494\t0\t0\t2\t1\t19\n+HG02597\tHG02597\t0\t0\t2\t1\t20\n+HG02600\tHG02600\t0\t0\t2\t1\t27\n+HG02601\tHG02601\t0\t0\t2\t1\t77\n+HG02603\tHG02603\t0\t0\t1\t1\t35\n+HG02604\tHG02604\t0\t0\t1\t1\t66\n+HG02648\tHG02648\t0\t0\t1\t1\t71\n+HG02649\tHG02649\t0\t0\t2\t1\t25\n+HG02651\tHG02651\t0\t0\t1\t1\t62\n+HG02652\tHG02652\t0\t0\t1\t1\t58\n+HG02654\tHG02654\t0\t0\t2\t1\t11\n+HG02655\tHG02655\t0\t0\t2\t1\t8\n+HG02657\tHG02657\t0\t0\t2\t1\t32\n+HG02658\tHG02658\t0\t0\t1\t1\t76\n+HG02660\tHG02660\t0\t0\t2\t1\t38\n+HG02661\tHG02661\t0\t0\t1\t1\t29\n+HG02681\tHG02681\t0\t0\t1\t1\t72\n+HG02682\tHG02682\t0\t0\t2\t1\t80\n+HG02684\tHG02684\t0\t0\t2\t1\t20\n+HG02685\tHG02685\t0\t0\t2\t1\t48\n+HG02687\tHG02687\t0\t0\t2\t1\t60\n+HG02688\tHG02688\t0\t0\t2\t1\t17\n+HG02690\tHG02690\t0\t0\t2\t1\t66\n+HG02691\tHG02691\t0\t0\t1\t1\t64\n+HG02694\tHG02694\t0\t0\t2\t1\t14\n+HG02696\tHG02696\t0\t0\t2\t1\t14\n+HG02697\tHG02697\t0\t0\t1\t1\t73\n+HG02699\tHG02699\t0\t0\t1\t1\t27\n+HG02700\tHG02700\t0\t0\t1\t1\t2\n+HG02724\tHG02724\t0\t0\t2\t1\t38\n+HG02725\tHG02725\t0\t0\t2\t1\t47\n+HG02727\tHG02727\t0\t0\t1\t1\t52\n+HG02728\tHG02728\t0\t0\t2\t1\t78\n+HG02731\tHG02731\t0\t0\t2\t1\t71\n+HG02733\tHG02733\t0\t0\t2\t1\t80\n+HG02734\tHG02734\t0\t0\t1\t1\t54\n+HG02736\tHG02736\t0\t0\t2\t1\t19\n+HG02737\tHG02737\t0\t0\t2\t1\t56\n+HG02774\tHG02774\t0\t0\t1\t1\t7\n+HG02775\tHG02775\t0\t0\t1\t1\t21\n+HG02778\tHG02778\t0\t0\t2\t1\t35\n+HG02780\tHG02780\t0\t0\t1\t1\t31\n+HG02783\tHG02783\t0\t0\t2\t1\t33\n+HG02784\tHG02784\t0\t0\t1\t1\t32\n+HG02786\tHG02786\t0\t0\t2\t1\t50\n+HG02787\tHG02787\t0\t0\t2\t1\t17\n+HG02789\tHG02789\t0\t0\t2\t1\t66\n+HG02790\tHG02790\t0\t0\t1\t1\t42\n+HG02792\tHG02792\t0\t0\t2\t1\t57\n+HG02793\tHG02793\t0\t0\t1\t1\t74\n+HG03006\tHG03006\t0\t0\t1\t1\t76\n+HG03007\tHG03007\t0\t0\t2\t1\t6\n+HG03009\tHG03009\t0\t0\t1\t1\t70\n+HG03012\tHG03012\t0\t0\t2\t1\t26\n+HG03015\tHG03015\t0\t0\t1\t1\t8\n+HG03016\tHG03016\t0\t0\t1\t1\t34\n+HG03018\tHG03018\t0\t0\t2\t1\t76\n+HG03019\tHG03019\t0\t0\t1\t1\t15\n+HG03021\tHG03021\t0\t0\t2\t1\t3\n+HG03022\tHG03022\t0\t0\t2\t1\t42\n+HG03228\tHG03228\t0\t0\t2\t1\t55\n+HG03229\tHG03229\t0\t0\t2\t1\t15\n+HG03234\tHG03234\t0\t0\t1\t1\t58\n+HG03235\tHG03235\t0\t0\t2\t1\t37\n+HG03237\tHG03237\t0\t0\t1\t1\t30\n+HG03238\tHG03238\t0\t0\t2\t1\t5\n+HG03488\tHG03488\t0\t0\t1\t1\t45\n+HG03490\tHG03490\t0\t0\t2\t1\t34\n+HG03491\tHG03491\t0\t0\t1\t1\t72\n+HG03585\tHG03585\t0\t0\t2\t1\t10\n+HG03589\tHG03589\t0\t0\t1\t1\t24\n+HG03593\tHG03593\t0\t0\t1\t1\t21\n+HG03594\tHG03594\t0\t0\t1\t1\t73\n+HG03595\tHG03595\t0\t0\t2\t1\t46\n+HG03598\tHG03598\t0\t0\t2\t1\t4\n+HG03600\tHG03600\t0\t0\t1\t1\t9\n+HG03603\tHG03603\t0\t0\t1\t1\t38\n+HG03604\tHG03604\t0\t0\t1\t1\t47\n+HG03607\tHG03607\t0\t0\t2\t1\t37\n+HG03611\tHG03611\t0\t0\t1\t1\t42\n+HG03615\tHG03615\t0\t0\t1\t1\t57\n+HG03616\tHG03616\t0\t0\t2\t1\t6\n+HG03619\tHG03619\t0\t0\t2\t1\t17\n+HG03624\tHG03624\t0\t0\t1\t1\t40\n+HG03625\tHG03625\t0\t0\t2\t1\t9\n+HG03629\tHG03629\t0\t0\t2\t1\t72\n+HG03631\tHG03631\t0\t0\t2\t1\t50\n+HG03634\tHG03634\t0\t0\t1\t1\t17\n+HG03636\tHG03636\t0\t0\t1\t1\t49\n+HG03640\tHG03640\t0\t0\t2\t1\t19\n+HG03642\tHG03642\t0\t0\t2\t1\t55\n+HG03643\tHG03643\t0\t0\t2\t1\t45\n+HG03644\tHG03644\t0\t0\t1\t1\t51\n+HG03645\tHG03645\t0\t0\t2\t1\t23\n+HG03646\tHG03646\t0\t0\t1\t1\t37\n+HG03649\tHG03649\t0\t0\t2\t1\t76\n+HG03652\tHG03652\t0\t0\t2\t1\t55\n+HG03653\tHG03653\t0\t0\t1\t1\t12\n+HG03660\tHG03660\t0\t0\t1\t1\t49\n+HG03663\tHG03663\t0\t0\t1\t1\t54\n+HG03667\tHG03667\t0\t0\t1\t1\t24\n+HG03668\tHG03668\t0\t0\t1\t1\t53\n+HG03672\tHG03672\t0\t0\t2\t1\t30\n+HG03673\tHG03673\t0\t0\t2\t1\t3\n+HG03679\tHG03679\t0\t0\t2\t1\t43\n+HG03680\tHG03680\t0\t0\t1\t1\t17\n+HG03681\tHG03681\t0\t0\t1\t1\t37\n+HG03684\tHG03684\t0\t0\t1\t1\t77\n+HG03685\tHG03685\t0\t0\t2\t1\t14\n+HG03686\tHG03686\t0\t0\t2\t1\t49\n+HG03687\tHG03687\t0\t0\t1\t1\t54\n+HG03689\tHG03689\t0\t0\t2\t1\t2\n+HG03690\tHG03690\t0\t0\t2\t1\t67\n+HG03691\tHG03691\t0\t0\t1\t1\t15\n+HG03692\tHG03692\t0\t0\t1\t1\t50\n+HG03693\tHG03693\t0\t0\t2\t1\t17\n+HG03694\tHG03694\t0\t0\t2\t1\t31\n+HG03695\tHG03695\t0\t0\t1\t1\t27\n+HG03696\tHG03696\t0\t0\t2\t1\t71\n+HG03697\tHG03697\t0\t0\t2\t1\t31\n+HG03698\tHG03698\t0\t0\t1\t1\t35\n+HG03702\tHG03702\t0\t0\t2\t1\t19\n+HG03703\tHG03703\t0\t0\t2\t1\t75\n+HG03705\tHG03705\t0\t0\t1\t1\t56\n+HG03706\tHG03706\t0\t0\t2\t1\t7\n+HG03708\tHG03708\t0\t0\t2\t1\t41\n+HG03709\tHG03709\t0\t0\t2\t1\t53\n+HG03711\tHG03711\t0\t0\t2\t1\t7\n+HG03713\tHG03713\t0\t0\t2\t1\t70\n+HG03714\tHG03714\t0\t0\t1\t1\t41\n+HG03716\tHG03716\t0\t0\t2\t1\t49\n+HG03717\tHG03717\t0\t0\t1\t1\t7\n+HG03718\tHG03718\t0\t0\t1\t1\t69\n+HG03720\tHG03720\t0\t0\t2\t1\t15\n+HG03722\tHG0'..b'0\t2\t2\t23\n+NA18616\tNA18616\t0\t0\t2\t2\t9\n+NA18617\tNA18617\t0\t0\t2\t2\t11\n+NA18618\tNA18618\t0\t0\t2\t2\t61\n+NA18619\tNA18619\t0\t0\t1\t2\t80\n+NA18620\tNA18620\t0\t0\t2\t2\t36\n+NA18621\tNA18621\t0\t0\t2\t2\t12\n+NA18622\tNA18622\t0\t0\t2\t2\t37\n+NA18623\tNA18623\t0\t0\t2\t2\t45\n+NA18624\tNA18624\t0\t0\t2\t2\t52\n+NA18625\tNA18625\t0\t0\t1\t2\t52\n+NA18626\tNA18626\t0\t0\t1\t2\t66\n+NA18627\tNA18627\t0\t0\t1\t2\t19\n+NA18628\tNA18628\t0\t0\t2\t2\t55\n+NA18629\tNA18629\t0\t0\t2\t2\t19\n+NA18630\tNA18630\t0\t0\t1\t2\t47\n+NA18631\tNA18631\t0\t0\t1\t2\t34\n+NA18632\tNA18632\t0\t0\t1\t2\t9\n+NA18633\tNA18633\t0\t0\t2\t2\t23\n+NA18634\tNA18634\t0\t0\t1\t2\t37\n+NA18635\tNA18635\t0\t0\t1\t2\t65\n+NA18636\tNA18636\t0\t0\t1\t2\t64\n+NA18637\tNA18637\t0\t0\t2\t2\t36\n+NA18638\tNA18638\t0\t0\t1\t2\t65\n+NA18639\tNA18639\t0\t0\t2\t2\t77\n+NA18640\tNA18640\t0\t0\t2\t2\t35\n+NA18641\tNA18641\t0\t0\t2\t2\t30\n+NA18642\tNA18642\t0\t0\t2\t2\t63\n+NA18643\tNA18643\t0\t0\t2\t2\t10\n+NA18644\tNA18644\t0\t0\t2\t2\t15\n+NA18645\tNA18645\t0\t0\t2\t2\t34\n+NA18646\tNA18646\t0\t0\t2\t2\t72\n+NA18647\tNA18647\t0\t0\t1\t2\t79\n+NA18648\tNA18648\t0\t0\t2\t2\t71\n+NA18740\tNA18740\t0\t0\t1\t2\t51\n+NA18745\tNA18745\t0\t0\t1\t2\t42\n+NA18747\tNA18747\t0\t0\t2\t2\t68\n+NA18748\tNA18748\t0\t0\t2\t2\t53\n+NA18749\tNA18749\t0\t0\t1\t2\t64\n+NA18757\tNA18757\t0\t0\t2\t2\t5\n+NA18939\tNA18939\t0\t0\t1\t2\t39\n+NA18940\tNA18940\t0\t0\t2\t2\t26\n+NA18941\tNA18941\t0\t0\t2\t2\t33\n+NA18942\tNA18942\t0\t0\t2\t2\t30\n+NA18943\tNA18943\t0\t0\t1\t2\t20\n+NA18944\tNA18944\t0\t0\t2\t2\t19\n+NA18945\tNA18945\t0\t0\t1\t2\t50\n+NA18946\tNA18946\t0\t0\t2\t2\t38\n+NA18947\tNA18947\t0\t0\t1\t2\t10\n+NA18948\tNA18948\t0\t0\t2\t2\t67\n+NA18949\tNA18949\t0\t0\t1\t2\t46\n+NA18950\tNA18950\t0\t0\t1\t2\t40\n+NA18951\tNA18951\t0\t0\t1\t2\t13\n+NA18952\tNA18952\t0\t0\t2\t2\t63\n+NA18953\tNA18953\t0\t0\t1\t2\t67\n+NA18954\tNA18954\t0\t0\t2\t2\t68\n+NA18956\tNA18956\t0\t0\t2\t2\t23\n+NA18957\tNA18957\t0\t0\t2\t2\t80\n+NA18959\tNA18959\t0\t0\t1\t2\t55\n+NA18960\tNA18960\t0\t0\t2\t2\t63\n+NA18961\tNA18961\t0\t0\t1\t2\t49\n+NA18962\tNA18962\t0\t0\t1\t2\t73\n+NA18963\tNA18963\t0\t0\t1\t2\t39\n+NA18964\tNA18964\t0\t0\t2\t2\t19\n+NA18965\tNA18965\t0\t0\t1\t2\t25\n+NA18966\tNA18966\t0\t0\t1\t2\t2\n+NA18967\tNA18967\t0\t0\t1\t2\t64\n+NA18968\tNA18968\t0\t0\t1\t2\t23\n+NA18969\tNA18969\t0\t0\t1\t2\t72\n+NA18970\tNA18970\t0\t0\t2\t2\t36\n+NA18971\tNA18971\t0\t0\t2\t2\t7\n+NA18972\tNA18972\t0\t0\t1\t2\t14\n+NA18973\tNA18973\t0\t0\t2\t2\t5\n+NA18974\tNA18974\t0\t0\t2\t2\t24\n+NA18975\tNA18975\t0\t0\t2\t2\t7\n+NA18976\tNA18976\t0\t0\t2\t2\t57\n+NA18977\tNA18977\t0\t0\t1\t2\t64\n+NA18978\tNA18978\t0\t0\t1\t2\t7\n+NA18979\tNA18979\t0\t0\t1\t2\t43\n+NA18980\tNA18980\t0\t0\t1\t2\t16\n+NA18981\tNA18981\t0\t0\t2\t2\t3\n+NA18982\tNA18982\t0\t0\t1\t2\t20\n+NA18983\tNA18983\t0\t0\t2\t2\t12\n+NA18984\tNA18984\t0\t0\t2\t2\t40\n+NA18985\tNA18985\t0\t0\t2\t2\t69\n+NA18986\tNA18986\t0\t0\t2\t2\t45\n+NA18987\tNA18987\t0\t0\t2\t2\t15\n+NA18988\tNA18988\t0\t0\t2\t2\t29\n+NA18989\tNA18989\t0\t0\t1\t2\t54\n+NA18990\tNA18990\t0\t0\t2\t2\t73\n+NA18991\tNA18991\t0\t0\t2\t2\t61\n+NA18992\tNA18992\t0\t0\t2\t2\t70\n+NA18993\tNA18993\t0\t0\t2\t2\t33\n+NA18994\tNA18994\t0\t0\t2\t2\t26\n+NA18995\tNA18995\t0\t0\t2\t2\t21\n+NA18997\tNA18997\t0\t0\t2\t2\t42\n+NA18998\tNA18998\t0\t0\t2\t2\t52\n+NA18999\tNA18999\t0\t0\t2\t2\t39\n+NA19000\tNA19000\t0\t0\t2\t2\t70\n+NA19001\tNA19001\t0\t0\t2\t2\t34\n+NA19002\tNA19002\t0\t0\t1\t2\t8\n+NA19003\tNA19003\t0\t0\t2\t2\t70\n+NA19004\tNA19004\t0\t0\t1\t2\t8\n+NA19005\tNA19005\t0\t0\t2\t2\t46\n+NA19006\tNA19006\t0\t0\t2\t2\t72\n+NA19007\tNA19007\t0\t0\t1\t2\t64\n+NA19009\tNA19009\t0\t0\t2\t2\t61\n+NA19010\tNA19010\t0\t0\t2\t2\t40\n+NA19011\tNA19011\t0\t0\t2\t2\t2\n+NA19012\tNA19012\t0\t0\t1\t2\t54\n+NA19054\tNA19054\t0\t0\t2\t2\t21\n+NA19055\tNA19055\t0\t0\t2\t2\t60\n+NA19056\tNA19056\t0\t0\t1\t2\t19\n+NA19057\tNA19057\t0\t0\t2\t2\t73\n+NA19058\tNA19058\t0\t0\t2\t2\t51\n+NA19059\tNA19059\t0\t0\t1\t2\t41\n+NA19060\tNA19060\t0\t0\t1\t2\t68\n+NA19062\tNA19062\t0\t0\t1\t2\t3\n+NA19063\tNA19063\t0\t0\t2\t2\t29\n+NA19064\tNA19064\t0\t0\t1\t2\t14\n+NA19065\tNA19065\t0\t0\t1\t2\t20\n+NA19066\tNA19066\t0\t0\t1\t2\t45\n+NA19067\tNA19067\t0\t0\t1\t2\t26\n+NA19068\tNA19068\t0\t0\t2\t2\t33\n+NA19070\tNA19070\t0\t0\t1\t2\t14\n+NA19072\tNA19072\t0\t0\t2\t2\t11\n+NA19074\tNA19074\t0\t0\t2\t2\t35\n+NA19075\tNA19075\t0\t0\t2\t2\t18\n+NA19076\tNA19076\t0\t0\t1\t2\t73\n+NA19077\tNA19077\t0\t0\t2\t2\t54\n+NA19078\tNA19078\t0\t0\t2\t2\t34\n+NA19079\tNA19079\t0\t0\t2\t2\t57\n+NA19080\tNA19080\t0\t0\t2\t2\t77\n+NA19081\tNA19081\t0\t0\t1\t2\t68\n+NA19082\tNA19082\t0\t0\t1\t2\t30\n+NA19083\tNA19083\t0\t0\t1\t2\t77\n+NA19084\tNA19084\t0\t0\t1\t2\t74\n+NA19085\tNA19085\t0\t0\t2\t2\t4\n+NA19086\tNA19086\t0\t0\t1\t2\t63\n+NA19087\tNA19087\t0\t0\t1\t2\t23\n+NA19088\tNA19088\t0\t0\t2\t2\t29\n+NA19089\tNA19089\t0\t0\t1\t2\t44\n+NA19090\tNA19090\t0\t0\t1\t2\t34\n+NA19091\tNA19091\t0\t0\t2\t2\t24\n' |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c examples/geneset.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/geneset.txt Thu Aug 04 04:40:06 2016 -0400 |
| b |
| @@ -0,0 +1,2 @@ +set1 http://set1 CICP27 HES5 AGRN VWA1 WASH7P ACAP3 UBE2J2 CDK11A RN7SL657P ATAD3B +set2 http://set2 MIR6859-1 MIR6859-2 GNB1 RER1 SKI C1orf222 ARHGEF16 SLC35E2B HES4 LINC01128 AURKAIP1 ATAD3C \ No newline at end of file |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c examples/hg19_breast.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/hg19_breast.txt Thu Aug 04 04:40:06 2016 -0400 |
| b |
| b'@@ -0,0 +1,47796 @@\n+1\t12942094\t12942094\tG\tA\t1\n+1\t152883016\t152883016\tA\tG\t1\n+1\t173837392\t173837392\tAGGCA\t-\t1\n+1\t203191404\t203191404\tC\tT\t1\n+11\t89531510\t89531510\tC\tT\t1\n+4\t9784617\t9784617\tT\tC\t1\n+6\t34100851\t34100851\t-\tG\t1\n+1\t152081726\t152081726\tC\tT\t1\n+1\t152883009\t152883009\tT\tC\t1\n+1\t16255140\t16255140\tT\tG\t1\n+1\t16255142\t16255142\tG\tC\t1\n+1\t166927145\t166927145\tG\tA\t1\n+1\t171678834\t171678834\tG\tA\t1\n+1\t175097269\t175097269\tG\tA\t1\n+1\t186031088\t186031088\tC\tA\t1\n+1\t204924024\t204924024\tC\tA\t1\n+1\t21268004\t21268004\tG\tC\t1\n+1\t234553884\t234553884\tC\tT\t1\n+1\t234553935\t234553935\tG\tA\t1\n+10\t1058471\t1058471\tG\tC\t1\n+10\t46143950\t46143950\tC\tT\t1\n+10\t76982036\t76982036\tC\tG\t1\n+10\t86012643\t86012643\tC\tT\t1\n+11\t32954075\t32954075\tC\tT\t1\n+11\t59376180\t59376180\tG\tC\t1\n+11\t65835787\t65835787\tC\tT\t1\n+11\t65977843\t65977843\tG\tA\t1\n+12\t117669913\t117669913\tC\tT\t1\n+12\t123485369\t123485369\tC\tA\t1\n+12\t50746166\t50746166\tG\tC\t1\n+12\t92814847\t92814847\tC\tT\t1\n+13\t33627952\t33627952\tC\tT\t1\n+14\t20925406\t20925406\tC\tT\t1\n+14\t21992809\t21992809\tC\tG\t1\n+14\t50829725\t50829725\tC\tG\t1\n+14\t52520852\t52520852\tC\tT\t1\n+15\t100537601\t100537601\tC\tG\t1\n+15\t62202444\t62202444\tC\tG\t1\n+15\t64967841\t64967841\tG\tA\t1\n+16\t2815863\t2815863\tG\tC\t1\n+16\t58073982\t58073982\tC\tG\t1\n+17\t17957467\t17957467\tC\tT\t1\n+17\t26955466\t26955466\tC\tG\t1\n+17\t28748817\t28748817\tC\tT\t1\n+17\t57105827\t57105827\tC\tT\t1\n+17\t58024096\t58024096\tC\tA\t1\n+17\t7577106\t7577106\tG\tA\t1\n+17\t79563247\t79563247\tC\tG\t1\n+18\t8796229\t8796229\tG\tC\t1\n+19\t19136589\t19136589\tC\tA\t1\n+19\t37441932\t37441932\tG\tC\t1\n+19\t42791030\t42791030\tC\tT\t1\n+19\t44099419\t44099419\tG\tA\t1\n+19\t9062785\t9062785\tT\tC\t1\n+2\t130953785\t130953785\tC\tT\t1\n+2\t157183425\t157183425\tG\tA\t1\n+2\t231314378\t231314378\tG\tA\t1\n+2\t231314967\t231314967\tG\tC\t1\n+2\t24526705\t24526705\tG\tA\t1\n+2\t32678880\t32678880\tT\tG\t1\n+2\t55439929\t55439929\tC\tT\t1\n+2\t88890569\t88890569\tA\tG\t1\n+20\t36938973\t36938973\tC\tT\t1\n+21\t19685299\t19685299\tG\tA\t1\n+21\t34922772\t34922772\tC\tT\t1\n+22\t37898681\t37898681\tG\tC\t1\n+22\t38610477\t38610477\tG\tA\t1\n+23\t123197697\t123197697\tG\tC\t1\n+23\t138668603\t138668603\tC\tT\t1\n+23\t24197640\t24197640\tC\tG\t1\n+23\t27479117\t27479117\tC\tG\t1\n+23\t308072\t308072\tC\tT\t1\n+23\t37027730\t37027730\tC\tT\t1\n+23\t48823167\t48823167\tC\tA\t1\n+3\t15094075\t15094075\tC\tT\t1\n+3\t195510706\t195510706\tG\tA\t1\n+3\t21606070\t21606070\tG\tC\t1\n+3\t38812779\t38812779\tA\tC\t1\n+4\t17616360\t17616360\tC\tT\t1\n+4\t40351427\t40351427\tG\tA\t1\n+5\t112868687\t112868687\tG\tC\t1\n+5\t134010826\t134010826\tG\tC\t1\n+5\t167645662\t167645662\tG\tA\t1\n+5\t176721105\t176721105\tC\tG\t1\n+5\t226026\t226026\tG\tC\t1\n+5\t33982496\t33982496\tC\tT\t1\n+5\t56777819\t56777819\tC\tT\t1\n+6\t109721258\t109721258\tA\tG\t1\n+6\t135539052\t135539052\tG\tA\t1\n+6\t13625988\t13625988\tG\tA\t1\n+6\t139247600\t139247600\tC\tT\t1\n+6\t152772267\t152772267\tG\tC\t1\n+6\t17629707\t17629707\tG\tT\t1\n+6\t30680851\t30680851\tC\tG\t1\n+6\t33148086\t33148086\tG\tA\t1\n+6\t33371895\t33371895\tG\tA\t1\n+6\t42713445\t42713445\tC\tT\t1\n+6\t56044743\t56044743\tG\tA\t1\n+6\t7987072\t7987072\tC\tT\t1\n+7\t112724441\t112724441\tG\tC\t1\n+7\t12376890\t12376890\tG\tA\t1\n+7\t150690919\t150690919\tG\tC\t1\n+7\t26224617\t26224617\tC\tG\t1\n+7\t44155411\t44155411\tC\tG\t1\n+7\t82582628\t82582628\tC\tT\t1\n+8\t144403390\t144403390\tC\tG\t1\n+8\t144403540\t144403540\tC\tG\t1\n+8\t144644187\t144644187\tG\tA\t1\n+8\t66692036\t66692036\tC\tT\t1\n+8\t73848478\t73848478\tG\tT\t1\n+9\t115931682\t115931682\tC\tT\t1\n+9\t127693608\t127693608\tC\tT\t1\n+10\t116605972\t116605972\tA\tT\t1\n+11\t18194855\t18194855\tC\tT\t1\n+12\t124229239\t124229239\tG\tA\t1\n+14\t36005002\t36005002\tG\tT\t1\n+16\t50342651\t50342651\tC\tT\t1\n+17\t73142778\t73142778\tC\t-\t1\n+17\t78195586\t78195586\tC\tT\t1\n+18\t624924\t624924\tC\tA\t1\n+19\t38810837\t38810837\tT\tG\t1\n+19\t54313492\t54313492\tA\tG\t1\n+23\t3228603\t3228603\tC\tT\t1\n+3\t154858036\t154858036\tA\tT\t1\n+3\t178952085\t178952085\tA\tG\t1\n+3\t195513298\t195513298\tA\tG\t1\n+3\t38622673\t38622673\tC\tT\t1\n+4\t166199361\t166199361\tC\tG\t1\n+5\t1221908\t1221908\tT\tC\t1\n+5\t76649228\t76649228\tG\tA\t1\n+5\t88018601\t88018601\tG\tA\t1\n+6\t47749839\t47749839\tC\tT\t1\n+9\t139925442\t139925442\tG\tA\t1\n+1\t107600392\t107600392\tG\tT\t1\n+1\t120529684\t120529684\tTC\tCA\t1\n+1\t237893655\t237893655\tC\tA\t1\n+1\t889206\t889206\tG\tA\t1\n+1\t91404735\t91404735\tC\tA\t1\n+10\t51853140\t51853140\tC\tT\t1\n+10\t7844304\t7844304\tA\tT\t1\n+10\t95556884\t95556884\tA\tG\t1\n+11\t10585799\t10585799\tC\tT\t1\n+11\t108384826\t1083'..b'T\tA\t1\n+11\t6499366\t6499366\tT\tC\t1\n+12\t52636898\t52636898\tG\tC\t1\n+12\t71833917\t71833917\tG\tA\t1\n+14\t24032994\t24032994\tG\tT\t1\n+14\t81329196\t81329196\tG\tA\t1\n+15\t34655637\t34655637\tC\tT\t1\n+16\t30389183\t30389183\tT\tC\t1\n+17\t11597227\t11597227\tC\tG\t1\n+17\t7577061\t7577061\tCTTT\t-\t1\n+17\t900427\t900427\tA\tG\t1\n+19\t42126986\t42126986\tC\tT\t1\n+19\t49119337\t49119337\tG\tA\t1\n+19\t49878066\t49878066\tG\tA\t1\n+19\t57641241\t57641241\tG\tT\t1\n+2\t136566347\t136566347\tA\tG\t1\n+2\t167284443\t167284443\tC\tT\t1\n+2\t170134405\t170134405\tG\tT\t1\n+2\t176802242\t176802242\tG\tC\t1\n+2\t18736520\t18736520\tC\tG\t1\n+22\t24124523\t24124523\tG\tA\t1\n+23\t39931968\t39931968\tG\tA\t1\n+4\t119952720\t119952720\tG\tA\t1\n+4\t39301747\t39301747\tT\tC\t1\n+5\t140012442\t140012442\tG\tT\t1\n+5\t32090922\t32090922\tG\tC\t1\n+6\t33424124\t33424124\tG\tA\t1\n+7\t20687685\t20687685\tC\tT\t1\n+8\t110655166\t110655166\tA\tG\t1\n+8\t145947814\t145947814\tC\tT\t1\n+8\t52321996\t52321996\tG\tT\t1\n+8\t95500959\t95500959\tC\tT\t1\n+9\t137623972\t137623972\tC\tT\t1\n+9\t139390869\t139390869\t-\tCCTGGCTC\t1\n+9\t139390877\t139390877\t-\tCCT\t1\n+9\t27949218\t27949218\tG\tA\t1\n+9\t2812275\t2812275\tG\tC\t1\n+1\t11119330\t11119330\tC\tG\t1\n+1\t151377893\t151377893\tC\tG\t1\n+1\t152681654\t152681654\tC\tT\t1\n+1\t15702190\t15702190\tG\tC\t1\n+1\t186026400\t186026400\tT\tC\t1\n+1\t204506608\t204506608\tA\tT\t1\n+1\t220752703\t220752703\tC\tG\t1\n+1\t22084163\t22084163\tC\tG\t1\n+1\t228495195\t228495195\tA\tT\t1\n+1\t99157223\t99157223\tG\tC\t1\n+10\t116602860\t116602860\tC\tT\t1\n+10\t123258049\t123258049\tG\tC\t1\n+10\t50340195\t50340195\tA\tT\t1\n+11\t129817174\t129817174\tC\tA\t1\n+11\t134104810\t134104810\tG\tT\t1\n+11\t4470851\t4470851\tA\tT\t1\n+11\t62561771\t62561771\tT\tC\t1\n+11\t67375917\t67375917\tT\tG\t1\n+12\t12300444\t12300444\tG\tA\t1\n+12\t14849213\t14849213\tG\tA\t1\n+13\t46619585\t46619585\tT\tG\t1\n+13\t98671984\t98671984\tT\tC\t1\n+14\t21024763\t21024763\tC\tT\t1\n+14\t23564377\t23564377\tC\tA\t1\n+14\t31598424\t31598424\tT\tG\t1\n+14\t69969563\t69969563\tC\tG\t1\n+14\t73198577\t73198577\tG\tA\t1\n+14\t92792293\t92792293\tC\tA\t1\n+15\t33955918\t33955918\tC\tT\t1\n+15\t63866266\t63866266\tC\tT\t1\n+15\t63866545\t63866545\tC\tT\t1\n+15\t86311723\t86311723\tA\tC\t1\n+16\t1129135\t1129135\tC\tT\t1\n+16\t68847304\t68847304\tG\tT\t1\n+16\t74946204\t74946204\tG\tC\t1\n+17\t39596964\t39596964\tC\tT\t1\n+17\t39622349\t39622349\tG\tT\t1\n+17\t67081246\t67081246\tC\tT\t1\n+17\t76567383\t76567383\tG\tA\t1\n+19\t14805918\t14805918\tG\tC\t1\n+19\t14829928\t14829928\tC\tT\t1\n+19\t21365513\t21365513\tA\tG\t1\n+19\t50193508\t50193508\tC\tG\t1\n+19\t52579393\t52579393\tT\tG\t1\n+2\t179442485\t179442485\tT\tC\t1\n+2\t179474059\t179474059\tG\tT\t1\n+2\t208865794\t208865794\tC\tA\t1\n+2\t219873785\t219873785\tG\tC\t1\n+2\t225738767\t225738767\tG\tT\t1\n+2\t26693990\t26693990\tA\tC\t1\n+2\t55795499\t55795499\tC\tT\t1\n+2\t74883757\t74883757\tC\tT\t1\n+2\t77746784\t77746784\tT\tA\t1\n+2\t85850804\t85850804\tG\tA\t1\n+20\t40118637\t40118637\tC\tG\t1\n+21\t35258721\t35258721\tC\tG\t1\n+22\t19052401\t19052401\tC\tA\t1\n+22\t42177711\t42177711\tC\tT\t1\n+23\t107436869\t107436869\tG\tT\t1\n+23\t122319694\t122319694\tC\tA\t1\n+23\t135767916\t135767916\tC\tG\t1\n+23\t18221806\t18221806\tG\tC\t1\n+23\t18342120\t18342120\tT\tC\t1\n+23\t18961899\t18961899\tC\tA\t1\n+23\t49074448\t49074448\tA\tT\t1\n+23\t53966853\t53966853\tT\tA\t1\n+23\t5821686\t5821686\tC\tT\t1\n+3\t100373936\t100373936\tT\tA\t1\n+3\t111319651\t111319651\tG\tT\t1\n+3\t152880777\t152880777\tC\tT\t1\n+3\t155210555\t155210555\tG\tA\t1\n+3\t186459878\t186459878\tG\tA\t1\n+3\t195480096\t195480096\tC\tA\t1\n+3\t57419473\t57419473\tG\tA\t1\n+3\t97167503\t97167503\tA\tC\t1\n+4\t151749586\t151749586\tC\tT\t1\n+4\t169317267\t169317267\tT\tA\t1\n+4\t187628565\t187628565\tC\tT\t1\n+5\t129040064\t129040064\tC\tT\t1\n+5\t140710475\t140710475\tT\tC\t1\n+5\t156957818\t156957818\tA\tG\t1\n+5\t178552030\t178552030\tG\tA\t1\n+5\t180429676\t180429676\tG\tA\t1\n+5\t55248110\t55248110\tG\tC\t1\n+5\t74640149\t74640149\tA\tG\t1\n+6\t105581324\t105581324\tC\tA\t1\n+6\t117632212\t117632212\tG\tC\t1\n+6\t132618423\t132618423\tC\tG\t1\n+6\t147122985\t147122985\tG\tA\t1\n+6\t25600888\t25600888\tC\tT\t1\n+7\t100647835\t100647835\tC\tG\t1\n+7\t107572731\t107572731\tC\tT\t1\n+7\t151071305\t151071305\tC\tT\t1\n+7\t16744257\t16744257\tG\tT\t1\n+7\t21775366\t21775366\tA\tG\t1\n+7\t23793941\t23793941\tG\tT\t1\n+7\t43484164\t43484164\tG\tT\t1\n+7\t6661429\t6661429\tG\tT\t1\n+7\t72849811\t72849811\tG\tA\t1\n+7\t77756528\t77756528\tA\tT\t1\n+8\t10285774\t10285774\tC\tT\t1\n+8\t125131850\t125131850\tG\tA\t1\n+8\t143561149\t143561149\tG\tA\t1\n+8\t3200906\t3200906\tG\tT\t1\n+8\t63978530\t63978530\tC\tA\t1\n+9\t34657465\t34657465\tG\tA\t1\n' |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c examples/param.rare.disease.hg19.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/param.rare.disease.hg19.txt Thu Aug 04 04:40:06 2016 -0400 |
| b |
| @@ -0,0 +1,57 @@ +#one argument per line +#I.Environmental setting +--buildver hg19 \ \ #line 1 +--nt 4 \ \ #line 2 +#--no-lib-check \ #line 3 +#--no-resource-check \ \ #line 4 + +#II. Specify the input files +--vcf-file examples/rare.disease.hg19.vcf \ #line 5 +--ped-file examples/rare.disease.ped.txt \ #line 6, or specify --indiv-pheno X:1,Y:1,Z:2 + +#III. Output setting +--out ./test1 \ #line 7 +--excel \ #line 8 +--o-vcf \ #line 10 +#--o-flanking-seq 50 \ #line 11, need large RAM memory + +#IV. QC +--gty-qual 10 \ #line 12 +--gty-dp 4 \ #line 13 +--gty-af-ref 0.05 \ #line 14 +--gty-af-het 0.25 \ #line 15 +--vcf-filter-in PASS,VQSRTrancheSNP90.00to93.00,VQSRTrancheSNP93.00to95.00,VQSRTrancheSNP95.00to97.00,VQSRTrancheSNP97.00to99.00 \ #line 16 +--seq-qual 50 \ #line 17 +--seq-mq 20 \ #line 18 +--seq-fs 60 \ #line 19 +--min-obsa 1 \ #line 20 +#V. Filtering + +--genotype-filter 1,2,6 \ #line 22 for recessive mode +#--ibs-case-filter 1000 \ #line 23, or specify 'ibdregions.txt' file +--regions-out chrX,chrY \ #line 22 +--db-filter 1kg201204,dbsnp141,ESP6500AA,ESP6500EA \ #line 26 +--rare-allele-freq 0.006 \ #line 27 +--db-filter-hard dbsnp138nf \ #line 27 +--db-gene refgene,gencode,knowngene \ #line 24 +--gene-feature-in 0,1,2,3,4,5,6 \ #line 25 +--superdup-filter \ +--gene-var-filter 4 + +#VI. Annotation +--scsnv-annot \#line 31 +--dgv-cnv-annot --candi-list ECEL1,MYBPC1,TNNI2,TNNT3,TPM2 \#line 31 +--geneset-annot cura \ #line 33 +--ppi-annot string \ #line 34 +--ppi-depth 1 \ #line 35 +--phenotype-term Arthrogryposis,Arthrogryposis+multiplex+congenita \ #line 35 +--pubmed-mining + +#VII. Prediction at variants +--db-score dbnsfp \ #line 28 +--mendel-causing-predict all +--filter-nondisease-variant \ #line 29 + +#VIII. Prediction at genes +--patho-gene-predict +#--phenolyzer-prediction \ No newline at end of file |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c examples/rare.disease.hg19.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/rare.disease.hg19.vcf Thu Aug 04 04:40:06 2016 -0400 |
| [ |
| b'@@ -0,0 +1,530 @@\n+##fileformat=VCFv4.0\r\n+##FILTER=<ID=LowQual,Description="Low quality">\r\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\r\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)">\r\n+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">\r\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\r\n+##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">\r\n+##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\r\n+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">\r\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\r\n+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">\r\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">\r\n+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">\r\n+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">\r\n+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">\r\n+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with two (and only two) segregating haplotypes">\r\n+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">\r\n+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">\r\n+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">\r\n+##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">\r\n+##SelectVariants="analysis_type=SelectVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null reference_sequence=/software/sequencing/GenomeAnalysisTK-1.0.5506/Homo_sapiens_assembly18.fasta rodBind=[/home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr1.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr2.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr3.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr4.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr5.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr6.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr7.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr8.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr9.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr10.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr11.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr12.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr13.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr14.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr15.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr16.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr17.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr18.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr19.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr20.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr21.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chr22.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chrX.vcf, /home/limx/myprojects/hbvexon/gatk/SNP/mergedsnps_chrY.vcf] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false DBSNP=null downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartPr'..b':99:420,0,605\t0/0:47,0:47:99:767,0,715\r\n+chr17\t9696199\trs8073531\tG\tC\t150.87\tPASS\tAC=2;AF=0.50;AN=4;DB;DP=2;Dels=0.00;HRun=2;HaplotypeScore=0.0427;MQ=118.63;MQ0=0;QD=25.14;SB=-25.88;sumGLbyD=37.63\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,606\t0/1:18,16:31:99:420,0,606\t0/0:47,0:47:99:767,0,716\r\n+chr17\t9696200\trs8074657\tC\tT\t149.89\tPASS\tAC=2;AF=0.50;AN=4;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0427;MQ=118.63;MQ0=0;QD=24.98;SB=-25.86;sumGLbyD=37.47\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,607\t0/1:18,16:31:99:420,0,607\t0/0:47,0:47:99:767,0,717\r\n+chr17\t9697803\t.\tG\tT\t225.32\tPASS\tAC=2;AF=1.00;AN=2;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0585;MQ=80.63;MQ0=0;QD=28.17;SB=-88.69;sumGLbyD=40.55\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,608\t0/1:18,16:31:99:420,0,608\t0/0:47,0:47:99:767,0,718\r\n+chr17\t9697822\trs3915463\tA\tC\t595.48\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.1667;MQ=77.70;MQ0=0;QD=29.77;SB=-294.36;sumGLbyD=34.23\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,609\t0/1:18,16:31:99:420,0,609\t0/0:47,0:47:99:767,0,719\r\n+chr17\t9698307\trs4791869\tC\tT\t468.92\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.1083;MQ=99.33;MQ0=0;QD=26.05;SB=-165.26;sumGLbyD=30.18\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,610\t0/1:18,16:31:99:420,0,610\t0/0:47,0:47:99:767,0,720\r\n+chr17\t9698396\trs4791870\tC\tT\t347.83\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=3;Dels=0.00;HRun=3;HaplotypeScore=0.2494;MQ=119.94;MQ0=0;QD=26.76;SB=-181.02;sumGLbyD=32.57\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,611\t0/1:18,16:31:99:420,0,611\t0/0:47,0:47:99:767,0,721\r\n+chr17\t9698688\t.\tA\tG\t68.41\tPASS\tAC=1;AF=0.25;AN=4;DP=3;Dels=0.00;HRun=0;HaplotypeScore=0.2179;MQ=82.48;MQ0=0;QD=11.40;SB=-22.66;sumGLbyD=21.93\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,612\t0/1:18,16:31:99:420,0,612\t0/0:47,0:47:99:767,0,722\r\n+chr17\t9699974\trs9913800\tT\tC\t207.88\tPASS\tAC=2;AF=0.50;AN=4;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=123.42;MQ0=0;QD=23.10;SB=-94.58;sumGLbyD=29.94\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,613\t0/1:18,16:31:99:420,0,613\t0/0:47,0:47:99:767,0,723\r\n+chr17\t9700198\trs2315587\tG\tA\t414.26\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=2;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=81.74;MQ0=0;QD=31.87;SB=-164.97;sumGLbyD=35.56\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,614\t0/1:18,16:31:99:420,0,614\t0/0:47,0:47:99:767,0,724\r\n+chr17\t9701390\trs2277691\tT\tC\t442.44\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0968;MQ=80.96;MQ0=0;QD=26.03;SB=-172.57;sumGLbyD=30.43\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,615\t0/1:18,16:31:99:420,0,615\t0/0:47,0:47:99:767,0,725\r\n+chr17\t9702456\trs8064616\tT\tC\t357.4\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=83.59;MQ0=0;QD=27.49;SB=-176.79;sumGLbyD=32.09\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,616\t0/1:18,16:31:99:420,0,616\t0/0:47,0:47:99:767,0,726\r\n+chr17\t9703299\trs17207745\tG\tA\t110.55\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=83.00;MQ0=0;QD=18.43;SB=-28.48;sumGLbyD=29.70\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,617\t0/1:18,16:31:99:420,0,617\t0/0:47,0:47:99:767,0,727\r\n+chr17\t9703383\trs2315578\tT\tC\t523.48\tPASS\tAC=4;AF=1.00;AN=4;DB;DP=3;Dels=0.00;HRun=2;HaplotypeScore=0.0000;MQ=109.12;MQ0=0;QD=30.79;SB=-262.59;sumGLbyD=35.58\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,618\t0/1:18,16:31:99:420,0,618\t0/0:47,0:47:99:767,0,728\r\n+chr17\t9707044\trs9891232\tT\tC\t401.99\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=1;HaplotypeScore=0.0000;MQ=78.31;MQ0=0;QD=23.65;SB=-216.68;sumGLbyD=29.07\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,619\t0/1:18,16:31:99:420,0,619\t0/0:47,0:47:99:767,0,729\r\n+chr17\t9709793\trs9914056\tG\tA\t411.79\tPASS\tAC=2;AF=1.00;AN=2;DB;DP=1;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=86.07;MQ0=0;QD=25.74;SB=-227.09;sumGLbyD=30.16\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,620\t0/1:18,16:31:99:420,0,620\t0/0:47,0:47:99:767,0,730\r\n+chr17\t9712767\trs9912329\tA\tC\t284.87\tPASS\tAC=2;AF=0.50;AN=4;DB;DP=2;Dels=0.00;HRun=1;HaplotypeScore=0.0853;MQ=95.60;MQ0=0;QD=21.91;SB=-96.35;sumGLbyD=27.51\tGT:AD:DP:GQ:PL\t0/1:18,16:31:99:420,0,621\t0/1:18,16:31:99:420,0,621\t0/0:47,0:47:99:767,0,731\r\n' |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c examples/rare.disease.ped.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/examples/rare.disease.ped.txt Thu Aug 04 04:40:06 2016 -0400 |
| b |
| @@ -0,0 +1,3 @@ +1 Y 0 0 1 1 +1 Z 0 0 2 1 +1 X Y Z 1 2 \ No newline at end of file |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c kggseq_variant_selection.xml --- a/kggseq_variant_selection.xml Mon May 25 18:01:25 2015 -0400 +++ b/kggseq_variant_selection.xml Thu Aug 04 04:40:06 2016 -0400 |
| b |
| @@ -1,7 +1,7 @@ -<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.3"> +<tool id="kggseq_variant_selection" name="Variant selection with KGGSeq" version="1.4"> <description></description> <requirements> - <requirement type="package" version="0.8_20150423 ">kggseq</requirement> + <requirement type="package" version="1.0_0_20160412">kggseq</requirement> </requirements> <command> java -jar \$KGGSEQ_JAR_PATH/kggseq.jar @@ -13,6 +13,7 @@ --no-progress-check --out results --o-vcf +--no-gz --vcf-file $inputFile --ped-file $pedFile @@ -126,9 +127,16 @@ #end if $add_annotations.genome_annotation $add_annotations.omim_annotation - $add_annotations.cosmic_annotation + $add_annotations.cosmic_annotation + $add_annotations.scsnv_annotation + $add_annotations.dgv_cnv_annotation + $add_annotations.superdup_annotation + $add_annotations.mouse_pheno_annotation + $add_annotations.zebrafish_pheno_annotation + $add_annotations.ddd_annotation + $add_annotations.patho_gene_predict_annotation #if $add_annotations.pubmed_mining_gene - $add_annotations.pubmed_type "$add_annotations.pubmed_mining_gene" + --phenotype-term "$add_annotations.pubmed_mining_gene" --pubmed-mining #end if #if str($add_annotations.shared_genes.shared_genes_select) == "yes" --ppi-annot string @@ -277,7 +285,12 @@ <option value="no" selected="true">No</option> </param> <when value="yes"> - <param name="allele_freq_db" type="select" display="checkboxes" multiple="true" label="Select databases for allelic frequency filtering (--db-filter)"> + <param name="allele_freq_db" type="select" display="checkboxes" multiple="true" label="Select databases for allelic frequency filtering (--db-filter)"> + <option value="1kgeur201305">1KG EUR 201305: 495 subjects in the EUR panel of 1000 Genomes Project release in 2013 May (around 24.0 million sequence variants)</option> + <option value="1kgeas201305">1KG EAS 201305: 496 subjects in the EAS panel of 1000 Genomes Project release in 2013 May (around 23.5 million sequence variants)</option> + <option value="1kgafr201305">1KG AFR 201305: 645 subjects in the AFR panel of 1000 Genomes Project release in 2013 May (around 41.7 million sequence variants)</option> + <option value="1kgsas201305">1KG SAS 201305: 485 subjects in the SAS panel of 1000 Genomes Project release in 2013 May (around 26.7 million sequence variants)</option> + <option value="1kgamr201305">1KG AMR 201305: 346 subjects in the AMR panel of 1000 Genomes Project release in 2013 May (around 28.2 million sequence variants)</option> <option value="1kg201305" selected="true">1KG 201305: 1000 Genomes Project 2013 May release</option> <option value="1kg201204">1KG 201204: 1000 Genomes Project 2012 April release</option> <option value="1kgafr201204">1KG 201204 AFR: 1000 Genomes Project 2012 April release - African</option> @@ -347,13 +360,16 @@ <param name="o_flanking_seq" type="integer" value="" optional="true" label="Size in bp of flanking sequence to extract (--o-flanking-seq)" /> <param name="genome_annotation" type="boolean" truevalue="--genome-annot" falsevalue="" checked="true" label="Add genomic functional annotations (presudogenes, TFBS, enhancer, UniProt) (--genome-annot)" /> <param name="omim_annotation" type="boolean" truevalue="--omim-annot" falsevalue="" checked="true" label="Add OMIM annotation (--omim-annot)" /> - <param name="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" /> - <param name="pubmed_type" type="select" label="Text mining in PubMed: find co-mentions of the search terms specified below with"> - <option value="--pubmed-mining">The cytogenetic position of each variant (--pubmed-mining)</option> - <option value="--pubmed-mining-gene">The gene in which each variant is located (--pubmed-mining-gene)</option> - </param> + <param name="cosmic_annotation" type="boolean" truevalue="--cosmic-annot" falsevalue="" checked="true" label="Add COSMIC annotation (--cosmic-annot)" /> + <param name="scsnv_annotation" type="boolean" truevalue="--scsnv-annot" falsevalue="" checked="true" label="Potential of altering splicing (--scsnv-annot)" /> + <param name="dgv_cnv_annotation" type="boolean" truevalue="--dgv-cnv-annot" falsevalue="" checked="true" label="Map a variant against known structure variation (--dgv-cnv-annot)" /> + <param name="superdup_annotation" type="boolean" truevalue="--superdup-annot" falsevalue="" checked="true" label="Mark the variants in the super duplicate regions (--superdup-annot)" /> + <param name="mouse_pheno_annotation" type="boolean" truevalue="--mouse-pheno" falsevalue="" checked="true" label="Annotate the genes with known mouse phenotypes as reference (--mouse-pheno)" /> + <param name="zebrafish_pheno_annotation" type="boolean" truevalue="--zebrafish-pheno" falsevalue="" checked="true" label="Annotate the genes with known zebrafish phenotypes as reference (--zebrafish-pheno)" /> + <param name="ddd_annotation" type="boolean" truevalue="--ddd-annot" falsevalue="" checked="true" label="Annotate by disease names in Deciphering Developmental Disorders (DDD) study (--ddd-annot)" /> + <param name="patho_gene_predict_annotation" type="boolean" truevalue="--patho-gene-predict" falsevalue="" checked="true" label="Predict genes’ pathogenicity (--patho-gene-predict)" /> <param name="pubmed_mining_gene" type="text" label="Text mining in PubMed: search term(s) of interest (e.g. disease name)" help="A comma-separated list of search terms, each composed by plus-separated words, e.g. spinocerebellar+ataxia,other+search+term. If empty, no search will be performed" /> - <!-- Shared protein-protein interactions and pathways --> + <!-- Shared protein-protein interactions and pathways --> <conditional name="shared_genes"> <param name="shared_genes_select" type="select" label="Add annotations for shared interactions/pathways?"> <option value="yes">Yes</option> |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c righe_tolte.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/righe_tolte.txt Thu Aug 04 04:40:06 2016 -0400 |
| b |
| @@ -0,0 +1,15 @@ +<action type="shell_command">java -jar kggseq.jar --no-lib-check --resource-update --resource resources --buildver hg19 --db-filter 1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all --patho-gene-predict --dgv-cnv-annot --vcf-file examples-lite/rare.disease.hg19.vcf</action> + + +<action type="shell_command">java -Xmx4g -jar kggseq.jar --no-lib-check --no-qc --resource-update --resource resources --buildver hg19 --o-flanking-seq 10 --vcf-file examples-lite/rare.disease.hg19.vcf</action> + + + + + + + +questa riga sottostante è l'unione delle due sopra e sarà quella definitiva + + +<action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kgeur201305,1kgeas201305,1kgafr201305,1kgsas201305,1kgamr201305,1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all --patho-gene-predict --dgv-cnv-annot --o-flanking-seq 10 --vcf-file examples-lite/rare.disease.hg19.vcf</action> \ No newline at end of file |
| b |
| diff -r c758125c56d8 -r a13b8ff61c6c tool_dependencies.xml --- a/tool_dependencies.xml Mon May 25 18:01:25 2015 -0400 +++ b/tool_dependencies.xml Thu Aug 04 04:40:06 2016 -0400 |
| b |
| @@ -1,12 +1,10 @@ <?xml version="1.0"?> <tool_dependency> - <package name="kggseq" version="0.8_20150423"> + <package name="kggseq" version="1.0_20160412"> <install version="1.0"> <actions> - <action type="download_by_url" target_filename="kggseq_archive-v0.8_20150423.tar.gz">https://github.com/crs4/kggseq_archive/archive/v0.8_20150423.tar.gz</action> - <action type="shell_command">touch test.vcf</action> - <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --vcf-file test.vcf</action> - <action type="shell_command">java -Xmx4g -jar kggseq.jar --no-lib-check --no-qc --resource resources --buildver hg19 --o-flanking-seq 10 --vcf-file examples/rare.disease.hg19.vcf</action> + <action type="download_by_url" target_filename="kggseq_archive-v1.0_20160412.tar.gz">https://github.com/crs4/kggseq_archive/archive/v1.0_20160412.tar.gz</action> + <action type="shell_command">java -jar kggseq.jar --no-lib-check --resource resources --buildver hg19 --db-filter 1kgeur201305,1kgeas201305,1kgafr201305,1kgsas201305,1kgamr201305,1kg201305,1kg201204,1kgafr201204,1kgeur201204,1kgamr201204,1kgasn201204,dbsnp135,dbsnp137,dbsnp138,dbsnp138nf,dbsnp141,ESP6500AA,ESP6500EA,exac --genome-annot --db-gene refgene,gencode,knowngene,ensembl --db-score dbnsfp --superdup-annot --cosmic-annot --omim-annot --scsnv-annot --mouse-pheno --zebrafish-pheno --ddd-annot --mendel-causing-predict all --patho-gene-predict --dgv-cnv-annot --o-flanking-seq 10 --vcf-file examples-lite/rare.disease.hg19.vcf</action> <action type="move_directory_files"> <source_directory>.</source_directory> <destination_directory>$INSTALL_DIR</destination_directory> |