Repository 'snpeff'
hg clone https://toolshed.g2.bx.psu.edu/repos/pcingola/snpeff

Changeset 0:481a95ca5339 (2011-06-07)
Next changeset 1:2cf01e805427 (2011-06-07)
Commit message:
Migrated tool version 0.9 from old tool shed archive to new tool shed repository
added:
._snpEff
snpEff/._data
snpEff/._scripts
snpEff/._snpEff.config
snpEff/._snpEff.xml
snpEff/README
snpEff/buildDb.jar
snpEff/data/._hg37
snpEff/data/._mm37
snpEff/data/hg37/._genes.txt
snpEff/data/hg37/._snpEffectPredictor.bin
snpEff/data/hg37/genes.txt
snpEff/data/hg37/snpEffectPredictor.bin
snpEff/data/mm37/._genes.txt
snpEff/data/mm37/._snpEffectPredictor.bin
snpEff/data/mm37/genes.txt
snpEff/data/mm37/snpEffectPredictor.bin
snpEff/scripts/._genes_hg37.xml
snpEff/scripts/._genes_mm37.xml
snpEff/scripts/._queryBiomart.pl
snpEff/scripts/genes_hg37.xml
snpEff/scripts/genes_mm37.xml
snpEff/scripts/queryBiomart.pl
snpEff/snpEff.config
snpEff/snpEff.jar
snpEff/snpEff.xml
b
diff -r 000000000000 -r 481a95ca5339 ._snpEff
b
Binary file ._snpEff has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/._data
b
Binary file snpEff/._data has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/._scripts
b
Binary file snpEff/._scripts has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/._snpEff.config
b
Binary file snpEff/._snpEff.config has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/._snpEff.xml
b
Binary file snpEff/._snpEff.xml has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff/README Tue Jun 07 17:08:59 2011 -0400
b
@@ -0,0 +1,31 @@
+
+snpEff Install details:
+-----------------------
+
+  By default the snpEff is assumed to be installed in /usr/local/snpEff
+  If you install it somewhere else, you'll need to modify the following files:
+
+ - snpEff.config:
+
+ ---------- Change data_dir param ----------
+ # Interval data is stored here
+ data_dir = /usr/local/snpEff/data/
+ ---------- End of change ----------
+
+ - snpEff.xml: This is the galaxy configuration file (in tools directory)
+
+ ---------- Change command param ----------
+ <command>java -jar /usr/local/snpEff/snpEff.jar -c /usr/local/snpEff/snpEff.config $genomeVersion $input > $output</command>
+ ---------- End of change ----------
+
+ WARNING!: You may need to use a custom memory value in your java virtual machine ("-XmX" option) as shown here:
+
+ ---------- Change command param ----------
+ <command>java -Xmx2048M -jar /usr/local/snpEff/snpEff.jar -c /usr/local/snpEff/snpEff.config $genomeVersion $input > $output</command>
+ ---------- End of change ----------
+
+If you have any bugs, suggestions or problems, you may contact me pablo.cingolani@mcgill.ca
+Enjoy!
+
+ Pablo Cingolani
+
b
diff -r 000000000000 -r 481a95ca5339 snpEff/buildDb.jar
b
Binary file snpEff/buildDb.jar has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/._hg37
b
Binary file snpEff/data/._hg37 has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/._mm37
b
Binary file snpEff/data/._mm37 has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/hg37/._genes.txt
b
Binary file snpEff/data/hg37/._genes.txt has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/hg37/._snpEffectPredictor.bin
b
Binary file snpEff/data/hg37/._snpEffectPredictor.bin has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/hg37/genes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff/data/hg37/genes.txt Tue Jun 07 17:08:59 2011 -0400
b
b'@@ -0,0 +1,1037096 @@\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000263100\t58858172\t58864865\tENSE00000729221\t58861736\t58862017\t6\t\t\t\t\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000263100\t58858172\t58864865\tENSE00000729227\t58862757\t58863053\t5\t\t\t\t\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000263100\t58858172\t58864865\tENSE00001169894\t58864658\t58864693\t2\t\t\t\t\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000263100\t58858172\t58864865\tENSE00001247354\t58863649\t58863921\t4\t\t\t\t\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000263100\t58858172\t58864865\tENSE00001247365\t58864294\t58864563\t3\t\t\t\t\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000263100\t58858172\t58864865\tENSE00001247383\t58864770\t58864865\t1\t58864804\t58864865\t\t\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000263100\t58858172\t58864865\tENSE00001309740\t58858719\t58859006\t7\t\t\t\t\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000263100\t58858172\t58864865\tENSE00001658053\t58858172\t58858395\t8\t\t\t58858172\t58858387\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000453054\t58858172\t58863159\tENSE00000729221\t58861736\t58862017\t2\t\t\t\t\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000453054\t58858172\t58863159\tENSE00001309740\t58858719\t58859006\t3\t\t\t\t\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000453054\t58858172\t58863159\tENSE00001658053\t58858172\t58858395\t4\t\t\t58858172\t58858387\n+A1BG\tENSG00000121410\t19\t58858172\t58864865\t-1\tprotein_coding\tENST00000453054\t58858172\t58863159\tENSE00001748944\t58862757\t58863159\t1\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00000986000\t52603748\t52603882\t4\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00000986001\t52601622\t52601752\t5\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00000986003\t52587891\t52588055\t7\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00000986004\t52580312\t52580409\t8\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00001093113\t52570800\t52570936\t11\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00001093114\t52573617\t52573822\t10\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00001093116\t52575766\t52576039\t9\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00001142847\t52569654\t52569802\t12\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00001345617\t52623793\t52623840\t2\t52623793\t52623840\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00001345621\t52566327\t52566640\t13\t\t\t52566327\t52566488\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00001345632\t52645341\t52645435\t1\t52645341\t52645435\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00002047706\t52595834\t52596072\t6\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000282641\t52566327\t52645435\tENSE00002053910\t52619602\t52619745\t3\t52619701\t52619745\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000373993\t52566322\t52619745\tENSE00000986000\t52603748\t52603882\t2\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000373993\t52566322\t52619745\tENSE00000986001\t52601622\t52601752\t3\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000373993\t52566322\t52619745\tENSE00000986003\t52587891\t52588055\t5\t\t\t\t\n+A1CF\tENSG00000148584\t10\t52566322\t52645435\t-1\tprotein_coding\tENST00000373993\t5256'..b'78028101\t78149104\t-1\tprotein_coding\tENST00000474746\t78047503\t78050744\tENSE00001857263\t78050452\t78050514\t2\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000474746\t78047503\t78050744\tENSE00001865229\t78050202\t78050340\t3\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000474746\t78047503\t78050744\tENSE00001912123\t78047664\t78047811\t4\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000474746\t78047503\t78050744\tENSE00001957870\t78050594\t78050744\t1\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476195\t78046703\t78050728\tENSE00001865229\t78050202\t78050340\t2\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476195\t78046703\t78050728\tENSE00001875182\t78047461\t78047573\t4\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476195\t78046703\t78050728\tENSE00001900108\t78046703\t78046754\t5\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476195\t78046703\t78050728\tENSE00001912123\t78047664\t78047811\t3\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476195\t78046703\t78050728\tENSE00001937183\t78050452\t78050728\t1\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001821429\t78041753\t78041905\t7\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001833610\t78045212\t78046754\t5\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001845711\t78047461\t78047576\t4\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001862809\t78030191\t78031469\t10\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001865229\t78050202\t78050340\t2\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001874222\t78097535\t78098561\t1\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001909285\t78034017\t78034151\t8\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001912123\t78047664\t78047811\t3\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001912506\t78031766\t78031866\t9\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000476275\t78030191\t78098561\tENSE00001941744\t78044459\t78044554\t6\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001821429\t78041753\t78041905\t8\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001831678\t78028101\t78031469\t11\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001865229\t78050202\t78050340\t2\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001875182\t78047461\t78047573\t4\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001877300\t78097535\t78097606\t1\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001909285\t78034017\t78034151\t9\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001912123\t78047664\t78047811\t3\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001912506\t78031766\t78031866\t10\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001933063\t78045212\t78045313\t6\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001934082\t78046683\t78046754\t5\t\t\t\t\n+ZZZ3\tENSG00000036549\t1\t78028101\t78149104\t-1\tprotein_coding\tENST00000481346\t78028101\t78097606\tENSE00001941744\t78044459\t78044554\t7\t\t\t\t\n'
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/hg37/snpEffectPredictor.bin
b
Binary file snpEff/data/hg37/snpEffectPredictor.bin has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/mm37/._genes.txt
b
Binary file snpEff/data/mm37/._genes.txt has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/mm37/._snpEffectPredictor.bin
b
Binary file snpEff/data/mm37/._snpEffectPredictor.bin has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/mm37/genes.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff/data/mm37/genes.txt Tue Jun 07 17:08:59 2011 -0400
b
b'@@ -0,0 +1,600294 @@\n+CR974568.2\tENSMUSG00000079178\t12\t3791316\t3791750\t-1\tprotein_coding\tENSMUST00000111202\t3791316\t3791750\tENSMUSE00000687037\t3791316\t3791340\t2\t\t\t\t\n+CR974568.2\tENSMUSG00000079178\t12\t3791316\t3791750\t-1\tprotein_coding\tENSMUST00000111202\t3791316\t3791750\tENSMUSE00000687038\t3791722\t3791750\t1\t\t\t\t\n+1500015L24Rik\tENSMUSG00000053614\t19\t20479778\t20497275\t1\tprotein_coding\tENSMUST00000066183\t20479778\t20497275\tENSMUSE00000422749\t20496749\t20497275\t3\t\t\t20496989\t20497275\n+1500015L24Rik\tENSMUSG00000053614\t19\t20479778\t20497275\t1\tprotein_coding\tENSMUST00000066183\t20479778\t20497275\tENSMUSE00000422761\t20495566\t20495753\t2\t20495566\t20495720\t\t\n+1500015L24Rik\tENSMUSG00000053614\t19\t20479778\t20497275\t1\tprotein_coding\tENSMUST00000066183\t20479778\t20497275\tENSMUSE00000427769\t20479778\t20479840\t1\t20479778\t20479840\t\t\n+AC174776.2\tENSMUSG00000078371\t12\t56300440\t56300832\t-1\tprotein_coding\tENSMUST00000105163\t56300440\t56300832\tENSMUSE00000665314\t56300440\t56300832\t1\t\t\t\t\n+AC115117.1\tENSMUSG00000073610\t18\t33623817\t33634364\t1\tprotein_coding\tENSMUST00000097634\t33623817\t33634364\tENSMUSE00000659763\t33632068\t33634364\t3\t\t\t33632103\t33634364\n+AC115117.1\tENSMUSG00000073610\t18\t33623817\t33634364\t1\tprotein_coding\tENSMUST00000097634\t33623817\t33634364\tENSMUSE00000659764\t33630430\t33630534\t2\t\t\t\t\n+AC115117.1\tENSMUSG00000073610\t18\t33623817\t33634364\t1\tprotein_coding\tENSMUST00000097634\t33623817\t33634364\tENSMUSE00000659765\t33623817\t33624126\t1\t\t\t\t\n+Fam70b\tENSMUSG00000038457\t8\t13435426\t13461369\t1\tprotein_coding\tENSMUST00000044736\t13435426\t13461369\tENSMUSE00000375794\t13461205\t13461369\t9\t\t\t\t\n+Fam70b\tENSMUSG00000038457\t8\t13435426\t13461369\t1\tprotein_coding\tENSMUST00000044736\t13435426\t13461369\tENSMUSE00000610172\t13456951\t13457094\t8\t\t\t\t\n+Fam70b\tENSMUSG00000038457\t8\t13435426\t13461369\t1\tprotein_coding\tENSMUST00000044736\t13435426\t13461369\tENSMUSE00000397701\t13455913\t13456072\t7\t\t\t\t\n+Fam70b\tENSMUSG00000038457\t8\t13435426\t13461369\t1\tprotein_coding\tENSMUST00000044736\t13435426\t13461369\tENSMUSE00000394301\t13455129\t13455214\t6\t\t\t\t\n+Fam70b\tENSMUSG00000038457\t8\t13435426\t13461369\t1\tprotein_coding\tENSMUST00000044736\t13435426\t13461369\tENSMUSE00000610173\t13454161\t13454241\t5\t\t\t\t\n+Fam70b\tENSMUSG00000038457\t8\t13435426\t13461369\t1\tprotein_coding\tENSMUST00000044736\t13435426\t13461369\tENSMUSE00000272242\t13451032\t13451115\t4\t\t\t\t\n+Fam70b\tENSMUSG00000038457\t8\t13435426\t13461369\t1\tprotein_coding\tENSMUST00000044736\t13435426\t13461369\tENSMUSE00000685592\t13451026\t13451030\t3\t\t\t\t\n+Fam70b\tENSMUSG00000038457\t8\t13435426\t13461369\t1\tprotein_coding\tENSMUST00000044736\t13435426\t13461369\tENSMUSE00000272250\t13441138\t13441280\t2\t\t\t\t\n+Fam70b\tENSMUSG00000038457\t8\t13435426\t13461369\t1\tprotein_coding\tENSMUST00000044736\t13435426\t13461369\tENSMUSE00000610175\t13435426\t13435667\t1\t\t\t\t\n+Gja3\tENSMUSG00000048582\t14\t57654497\t57676782\t-1\tprotein_coding\tENSMUST00000061614\t57654497\t57676782\tENSMUSE00000347502\t57654497\t57655767\t2\t57655751\t57655767\t\t\n+Gja3\tENSMUSG00000048582\t14\t57654497\t57676782\t-1\tprotein_coding\tENSMUST00000061614\t57654497\t57676782\tENSMUSE00000687312\t57676643\t57676782\t1\t57676643\t57676782\t\t\n+Tbca\tENSMUSG00000042043\t13\t95558898\t95612852\t1\tprotein_coding\tENSMUST00000046644\t95558898\t95612852\tENSMUSE00000452365\t95612605\t95612852\t4\t\t\t95612686\t95612852\n+Tbca\tENSMUSG00000042043\t13\t95558898\t95612852\t1\tprotein_coding\tENSMUST00000046644\t95558898\t95612852\tENSMUSE00000301686\t95607063\t95607149\t3\t\t\t\t\n+Tbca\tENSMUSG00000042043\t13\t95558898\t95612852\t1\tprotein_coding\tENSMUST00000046644\t95558898\t95612852\tENSMUSE00000301695\t95602315\t95602420\t2\t\t\t\t\n+Tbca\tENSMUSG00000042043\t13\t95558898\t95612852\t1\tprotein_coding\tENSMUST00000046644\t95558898\t95612852\tENSMUSE00000301703\t95558898\t95558957\t1\t95558898\t95558904\t\t\n+Olfr732\tENSMUSG00000057782\t14\t50901000\t50901926\t-1\tprotein_coding\tENSMUST00000075891\t50901000\t50901926\tENSMUSE00000520552\t50901000\t50901926\t1\t\t\t\t\n+AC131780.5\tENSMUSG00000079719\t9\t3020108\t3021593\t1\tprotein_coding\tENSMUST00000099047\t3020108\t3021593\tENSMUSE00000638885\t3021469\t3021593\t5\t\t\t\t\n+AC131780.5\tENSMUSG00000079719\t9\t3020108\t3021593\t1\tprotein_codin'..b'104377\t166890498\t166890586\tENSMUSE00000664530\t166890498\t166890586\t1\t\t\t\t\n+mmu-mir-21\tENSMUSG00000065455\t11\t86397569\t86397660\t-1\tmiRNA\tENSMUST00000083521\t86397569\t86397660\tENSMUSE00000522680\t86397569\t86397660\t1\t\t\t\t\n+U1\tENSMUSG00000065216\t6\t53383968\t53384131\t1\tsnRNA\tENSMUST00000083282\t53383968\t53384131\tENSMUSE00000522441\t53383968\t53384131\t1\t\t\t\t\n+mmu-mir-191\tENSMUSG00000065615\t9\t108470642\t108470732\t1\tmiRNA\tENSMUST00000083681\t108470642\t108470732\tENSMUSE00000522840\t108470642\t108470732\t1\t\t\t\t\n+SNORA38\tENSMUSG00000064853\t17\t35299508\t35299641\t-1\tsnoRNA\tENSMUST00000082919\t35299508\t35299641\tENSMUSE00000522077\t35299508\t35299641\t1\t\t\t\t\n+mmu-mir-487b\tENSMUSG00000076219\t12\t110965543\t110965624\t1\tmiRNA\tENSMUST00000102265\t110965543\t110965624\tENSMUSE00000660578\t110965543\t110965624\t1\t\t\t\t\n+7SK\tENSMUSG00000089621\t4\t53733774\t53734072\t-1\tmisc_RNA\tENSMUST00000158996\t53733774\t53734072\tENSMUSE00000848131\t53733774\t53734072\t1\t\t\t\t\n+mmu-mir-466b-1\tENSMUSG00000076992\t2\t10410516\t10410597\t1\tmiRNA\tENSMUST00000103804\t10410516\t10410597\tENSMUSE00000663957\t10410516\t10410597\t1\t\t\t\t\n+SNORA2\tENSMUSG00000064961\t2\t168161200\t168161336\t1\tsnoRNA\tENSMUST00000083027\t168161200\t168161336\tENSMUSE00000522186\t168161200\t168161336\t1\t\t\t\t\n+5S_rRNA\tENSMUSG00000089622\t17\t31196549\t31196676\t1\trRNA\tENSMUST00000158997\t31196549\t31196676\tENSMUSE00000848132\t31196549\t31196676\t1\t\t\t\t\n+AC153621.1\tENSMUSG00000089623\t6\t43789431\t43789507\t-1\tmiRNA\tENSMUST00000158998\t43789431\t43789507\tENSMUSE00000848133\t43789431\t43789507\t1\t\t\t\t\n+mmu-mir-544\tENSMUSG00000077001\t12\t110967535\t110967612\t1\tmiRNA\tENSMUST00000103813\t110967535\t110967612\tENSMUSE00000663966\t110967535\t110967612\t1\t\t\t\t\n+U6\tENSMUSG00000089624\t13\t14720886\t14720998\t-1\tsnRNA\tENSMUST00000158999\t14720886\t14720998\tENSMUSE00000848134\t14720886\t14720998\t1\t\t\t\t\n+mmu-mir-294\tENSMUSG00000077903\t7\t3220642\t3220725\t1\tmiRNA\tENSMUST00000104710\t3220642\t3220725\tENSMUSE00000664862\t3220642\t3220725\t1\t\t\t\t\n+U6\tENSMUSG00000065906\t3\t136730856\t136730962\t1\tsnRNA\tENSMUST00000083972\t136730856\t136730962\tENSMUSE00000523130\t136730856\t136730962\t1\t\t\t\t\n+mmu-mir-706\tENSMUSG00000076217\t6\t119984246\t119984329\t-1\tmiRNA\tENSMUST00000102262\t119984246\t119984329\tENSMUSE00000660576\t119984246\t119984329\t1\t\t\t\t\n+AC161212.2\tENSMUSG00000080646\t3\t145787283\t145787339\t1\tmiRNA\tENSMUST00000116996\t145787283\t145787339\tENSMUSE00000707898\t145787283\t145787339\t1\t\t\t\t\n+SCARNA18\tENSMUSG00000089625\t19\t11769757\t11769832\t1\tsnoRNA\tENSMUST00000159000\t11769757\t11769832\tENSMUSE00000848135\t11769757\t11769832\t1\t\t\t\t\n+AC136741.3\tENSMUSG00000080363\t7\t135969861\t135969981\t1\tmiRNA\tENSMUST00000116713\t135969861\t135969981\tENSMUSE00000707615\t135969861\t135969981\t1\t\t\t\t\n+AC141869.1\tENSMUSG00000078006\t8\t105256290\t105256384\t-1\tmiRNA\tENSMUST00000104813\t105256290\t105256384\tENSMUSE00000664962\t105256290\t105256384\t1\t\t\t\t\n+AC159290.1\tENSMUSG00000080451\t13\t61924904\t61925024\t-1\tmiRNA\tENSMUST00000116801\t61924904\t61925024\tENSMUSE00000707703\t61924904\t61925024\t1\t\t\t\t\n+AL772216.35\tENSMUSG00000077054\t2\t10405309\t10405405\t1\tmiRNA\tENSMUST00000103866\t10405309\t10405405\tENSMUSE00000664019\t10405309\t10405405\t1\t\t\t\t\n+SNORA17\tENSMUSG00000077379\tX\t127449835\t127449963\t-1\tsnoRNA\tENSMUST00000104191\t127449835\t127449963\tENSMUSE00000664344\t127449835\t127449963\t1\t\t\t\t\n+U6\tENSMUSG00000075833\t12\t4765353\t4765459\t1\tsnRNA\tENSMUST00000101885\t4765353\t4765459\tENSMUSE00000660199\t4765353\t4765459\t1\t\t\t\t\n+mmu-mir-370\tENSMUSG00000065433\t12\t110856468\t110856546\t1\tmiRNA\tENSMUST00000083499\t110856468\t110856546\tENSMUSE00000522658\t110856468\t110856546\t1\t\t\t\t\n+SNORA70\tENSMUSG00000089626\t8\t48525772\t48525905\t1\tsnoRNA\tENSMUST00000159001\t48525772\t48525905\tENSMUSE00000848136\t48525772\t48525905\t1\t\t\t\t\n+AL833773.1\tENSMUSG00000077037\t4\t93405427\t93405536\t1\tmiRNA\tENSMUST00000103849\t93405427\t93405536\tENSMUSE00000664002\t93405427\t93405536\t1\t\t\t\t\n+SNORA17\tENSMUSG00000077476\t17\t12493902\t12494041\t1\tsnoRNA\tENSMUST00000104288\t12493902\t12494041\tENSMUSE00000664441\t12493902\t12494041\t1\t\t\t\t\n+AC154908.1\tENSMUSG00000080642\t12\t82699121\t82699211\t1\tmiRNA\tENSMUST00000116992\t82699121\t82699211\tENSMUSE00000707894\t82699121\t82699211\t1\t\t\t\t\n'
b
diff -r 000000000000 -r 481a95ca5339 snpEff/data/mm37/snpEffectPredictor.bin
b
Binary file snpEff/data/mm37/snpEffectPredictor.bin has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/scripts/._genes_hg37.xml
b
Binary file snpEff/scripts/._genes_hg37.xml has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/scripts/._genes_mm37.xml
b
Binary file snpEff/scripts/._genes_mm37.xml has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/scripts/._queryBiomart.pl
b
Binary file snpEff/scripts/._queryBiomart.pl has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/scripts/genes_hg37.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff/scripts/genes_hg37.xml Tue Jun 07 17:08:59 2011 -0400
b
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE Query>
+<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
+ <Dataset name = "hsapiens_gene_ensembl" interface = "default" >
+ <Attribute name = "external_gene_id" />
+ <Attribute name = "ensembl_gene_id" />
+ <Attribute name = "chromosome_name" />
+ <Attribute name = "start_position" />
+ <Attribute name = "end_position" />
+ <Attribute name = "strand" />
+ <Attribute name = "gene_biotype" />
+ <Attribute name = "ensembl_transcript_id" />
+ <Attribute name = "transcript_start" />
+ <Attribute name = "transcript_end" />
+ <Attribute name = "ensembl_exon_id" />
+ <Attribute name = "exon_chrom_start" />
+ <Attribute name = "exon_chrom_end" />
+ <Attribute name = "rank" />
+ <Attribute name = "5_utr_start" />
+ <Attribute name = "5_utr_end" />
+ <Attribute name = "3_utr_start" />
+ <Attribute name = "3_utr_end" />
+ </Dataset>
+</Query>
b
diff -r 000000000000 -r 481a95ca5339 snpEff/scripts/genes_mm37.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff/scripts/genes_mm37.xml Tue Jun 07 17:08:59 2011 -0400
b
@@ -0,0 +1,24 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE Query>
+<Query  virtualSchemaName = "default" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
+ <Dataset name = "mmusculus_gene_ensembl" interface = "default" >
+ <Attribute name = "external_gene_id" />
+ <Attribute name = "ensembl_gene_id" />
+ <Attribute name = "chromosome_name" />
+ <Attribute name = "start_position" />
+ <Attribute name = "end_position" />
+ <Attribute name = "strand" />
+ <Attribute name = "gene_biotype" />
+ <Attribute name = "ensembl_transcript_id" />
+ <Attribute name = "transcript_start" />
+ <Attribute name = "transcript_end" />
+ <Attribute name = "ensembl_exon_id" />
+ <Attribute name = "exon_chrom_start" />
+ <Attribute name = "exon_chrom_end" />
+ <Attribute name = "rank" />
+ <Attribute name = "5_utr_start" />
+ <Attribute name = "5_utr_end" />
+ <Attribute name = "3_utr_start" />
+ <Attribute name = "3_utr_end" />
+ </Dataset>
+</Query>
b
diff -r 000000000000 -r 481a95ca5339 snpEff/scripts/queryBiomart.pl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff/scripts/queryBiomart.pl Tue Jun 07 17:08:59 2011 -0400
[
@@ -0,0 +1,25 @@
+#!/usr/bin/perl
+
+#------------------------------------------------------------------------------
+# An example script demonstrating the use of BioMart webservice
+#------------------------------------------------------------------------------
+
+use strict;
+use LWP::UserAgent;
+
+open (FH,$ARGV[0]) || die ("\nUsage: queryBiomart.pl Query.xml\n\n");
+my $xml;
+while (<FH>){ $xml .= $_; }
+close(FH);
+
+my $path="http://www.biomart.org/biomart/martservice?";
+my $request = HTTP::Request->new("POST",$path,HTTP::Headers->new(),'query='.$xml."\n");
+my $ua = LWP::UserAgent->new;
+
+my $response;
+$ua->request($request, 
+      sub {   
+  my($data, $response) = @_;
+  if ($response->is_success) { print "$data"; }
+  else { warn ("Problems with the web server: ".$response->status_line); }
+      } ,1000);
b
diff -r 000000000000 -r 481a95ca5339 snpEff/snpEff.config
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff/snpEff.config Tue Jun 07 17:08:59 2011 -0400
b
@@ -0,0 +1,32 @@
+
+# Interval data is stored here
+data_dir = /usr/local/snpEff/data/
+
+# Store cache files here
+cache_dir = /tmp
+
+# Comma separated list of genomes
+genomes : hg37, mm37
+
+# For each genome 'XX' a set of attributes are defined:
+#   - XX.genome             : The name of this genome
+# - XX.chromosomes        : A comma separated list of chromosome names
+# - XX.fasta_dir          : The directory where fasta files of this genome are located
+# - XX.chromo_fasta_files : A comma separated list of the fasta files (one per chromosome). 
+#                             WARNING: They must be in the same order as the XX.chromosomes list
+#
+# Note: Attributes XX.fasta_dir and XX.chromo_fasta_files are only needed if you are building the data 
+#       structures yourself. If you are using a pre-built file, you can leave both of them unassigned.
+
+
+# Human genome, version hg37
+hg37.genome : Human
+ hg37.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y
+ hg37.fasta_dir : /data/genomes/hg37/
+ hg37.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chr20.fa, chr21.fa, chr22.fa, chrX.fa, chrY.fa
+
+# Mouse genome, version mm37
+mm37.genome : Mouse
+ mm37.chromosomes : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X, Y
+ mm37.fasta_dir : /data/genomes/mm37/
+ mm37.chromo_fasta_files : chr1.fa, chr2.fa, chr3.fa, chr4.fa, chr5.fa, chr6.fa, chr7.fa, chr8.fa, chr9.fa, chr10.fa, chr11.fa, chr12.fa, chr13.fa, chr14.fa, chr15.fa, chr16.fa, chr17.fa, chr18.fa, chr19.fa, chrX.fa, chrY.fa
b
diff -r 000000000000 -r 481a95ca5339 snpEff/snpEff.jar
b
Binary file snpEff/snpEff.jar has changed
b
diff -r 000000000000 -r 481a95ca5339 snpEff/snpEff.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/snpEff/snpEff.xml Tue Jun 07 17:08:59 2011 -0400
[
@@ -0,0 +1,99 @@
+<tool id="snpEff" name="Compute SNP effect" version="0.9">
+ <description>for each SNP in a file</description>
+ <command>java -jar /usr/local/snpEff/snpEff.jar -c /usr/local/snpEff/snpEff.config $genomeVersion $input > $output</command>
+ <!-- <command>java -Xmx2048M -jar /usr/local/snpEff/snpEff.jar -c /usr/local/snpEff/snpEff.config $genomeVersion $input > $output</command> -->
+ <inputs>
+ <param format="interval" name="input" type="data" label="Source file"/>
+ <param name="genomeVersion" type="select" label="Genome">
+ <option value="hg37">Human (hg37)</option>
+ <option value="mm37">Mouse (mm37)</option>
+ </param>
+ </inputs>
+ <outputs>
+ <data format="tabular" name="output" />
+ </outputs>
+
+ <help>
+
+This tool computes the effect of SNPs. Current predictions include
+
+ * GENE : ENSEMBL gene ID, gene name and bio-type
+ * TRANSCRIPT : ENSEMBL transcript ID
+ * INTRON : The SNP hits a transcript, but no exons (or UTRs)
+ * EXON : ENSEMBL exon ID
+ * SYNONYMOUS_CODING : The SNP changes the DNA sequence in a way that produces the same amino acid
+ * NON_SYNONYMOUS_CODING : The SNP changes the DNA sequence in a way that produces a different amino acid
+ * STOP_GAINED : The SNP creates a new STOP codon
+ * STOP_LOST : The SNP changes a STOP codon into an amino acid
+ * UPSTREAM : The SNP is 2K bases upstream of a transcript (before 5 prime UTR)
+ * DOWNSTREAM : The SNP is 2K bases downstream of a transcript (after 3 prime UTR)
+ * 5PRIME_UTR : The SNP is in the 5 prime UTR region
+ * 3PRIME_UTR : The SNP is in the 3 prime UTR region
+ * INTERGENIC : The SNP does not any known gene or up/downstream region
+
+-----
+
+.. class:: infomark
+
+**File format**
+
+The file format must be tab-separated format, containing five columns that correspond to:
+
+ * chromosome_name
+ * chromosome_start_position
+ * chromosome_end_position
+ * allele: "base_Ori / base_Snp"
+ * strand: {+,-}
+
+.. class:: warningmark 
+
+**WARNING** Insertions and deletions are not supported, so chromosome_start_position is equal to chromosome_end_position::
+ 
+-----
+
+.. class:: infomark
+
+**Input file format example**
+
+This is an example of an input file::
+
+    5   140532    140532    T/C   +
+    12  1017956   1017956   T/A   +
+    2   946507    946507    G/C   +
+    14  19584687  19584687  C/T   -
+    19  66520     66520     G/A   +
+    8   150029    150029    A/T   +
+
+-----
+
+.. class:: infomark
+
+**Output file format example**
+
+The output file consist of one line per SNP effect. This means that you usually get more than one line per SNP. The format is tab separated cinsisting of two columns
+
+ * SNP:  chr:position_besOri/baseSnp
+ * Effect : Effect[, EXON:ExonId, TRANSCRIPT:TranscriptId, GENE:GeneId (genenName bioType)]
+
+This is an example of an output file::
+
+    chr2:946507_G/C        UPSTREAM, ENST00000452177
+    chr2:946507_G/C        UPSTREAM, ENST00000450962
+    chr2:946507_G/C        UPSTREAM, ENST00000308624
+    chr2:946507_G/C        UPSTREAM, ENST00000407292
+    chr5:140532_T/C        NON_SYNONYMOUS_CODING (V/A), EXON:ENSE00001319336, TRANSCRIPT:ENST00000283426, GENE:ENSG00000153404(PLEKHG4B protein_coding)
+    chr5:140532_T/C        NON_SYNONYMOUS_CODING (V/A), EXON:ENSE00001319336, TRANSCRIPT:ENST00000398036, GENE:ENSG00000153404(PLEKHG4B protein_coding)
+    chr5:140532_T/C        DOWNSTREAM, ENST00000398036
+    chr8:150029_A/T        NON_SYNONYMOUS_CODING (Y/N), EXON:ENSE00001913609, TRANSCRIPT:ENST00000490482, GENE:ENSG00000223508(RPL23AP53 protein_coding)
+    chr12:1017956_T/A      STOP_LOST (*/K), EXON:ENSE00001527897, TRANSCRIPT:ENST00000340908, GENE:ENSG00000060237(WNK1 protein_coding)
+    chr12:1017956_T/A      STOP_LOST (*/K), EXON:ENSE00001527897, TRANSCRIPT:ENST00000252477, GENE:ENSG00000060237(WNK1 protein_coding)
+    chr12:1017956_T/A      STOP_LOST (*/K), EXON:ENSE00001527897, TRANSCRIPT:ENST00000315939, GENE:ENSG00000060237(WNK1 protein_coding)
+    chr12:1017956_T/A      UPSTREAM, ENST00000340908
+    chr14:19584687_C/T     3PRIME_UTR, ENSE00001583193, TRANSCRIPT:ENST00000409832, GENE:ENSG00000222036(POTEG protein_coding)
+
+.. class:: warningmark 
+
+**WARNING** You may get the same effect on one exon repeated because it acts on different transcripts::
+ </help>
+</tool>
+