| 47e9f4e | gitliver | 29 May 2019, 16:26:36 UTC | add MIT License | 29 May 2019, 16:26:36 UTC |
| def1fb2 | timchu90 | 22 July 2016, 16:57:51 UTC | multiple changes unify case names when merging tavs remove ‘/‘ if last character in a directory fixed error when missing chromosomes Y or MT | 22 July 2016, 16:57:51 UTC |
| ef05362 | timchu90 | 21 July 2016, 14:44:31 UTC | update readme | 21 July 2016, 14:44:31 UTC |
| a9b7727 | timchu90 | 21 July 2016, 14:23:01 UTC | fixed error checking on missing annovcf argument | 21 July 2016, 14:23:01 UTC |
| d6d02ee | timchu90 | 18 July 2016, 16:21:15 UTC | parallel filter step | 18 July 2016, 16:21:15 UTC |
| e7eca6e | timchu90 | 06 July 2016, 14:57:17 UTC | parallelized using cluster | 06 July 2016, 14:57:17 UTC |
| 8ab804b | timchu90 | 01 July 2016, 18:01:05 UTC | whoops | 01 July 2016, 18:01:05 UTC |
| 2213e25 | timchu90 | 01 July 2016, 17:27:30 UTC | slightly changed naming of intermediate files. now properly deleting intermediate files | 01 July 2016, 17:27:30 UTC |
| 2890a2a | timchu90 | 29 June 2016, 18:39:07 UTC | Merge branch 'varcall_filter-refactor' | 29 June 2016, 18:39:07 UTC |
| a7ce36f | timchu90 | 29 June 2016, 17:58:29 UTC | working parallelized | 29 June 2016, 17:58:29 UTC |
| 54b83a6 | timchu90 | 28 June 2016, 21:31:18 UTC | parallelized annotation step more testing needed | 28 June 2016, 21:31:18 UTC |
| a5d5298 | timchu90 | 28 June 2016, 14:28:38 UTC | Merge branch 'master' into varcall_filter-refactor # Conflicts: # TOBIvaf.py # varCall_filtering/scripts/helpers.py # varCall_filtering/scripts/helpers.pyc | 28 June 2016, 14:28:38 UTC |
| 0c348a4 | timchu90 | 27 June 2016, 21:42:06 UTC | temp commit. parallelizing annotation | 27 June 2016, 21:42:06 UTC |
| 67a16c4 | cjmadubata | 21 June 2016, 19:38:34 UTC | detect if ref file has chr, if/else to add chr to region flag | 21 June 2016, 19:38:34 UTC |
| 833de69 | timchu90 | 09 June 2016, 19:52:58 UTC | parallelized for each sample. uses multi-threading have not tested yet on large number of threads. | 09 June 2016, 19:52:58 UTC |
| 58fe836 | timchu90 | 18 May 2016, 21:53:42 UTC | added readme description, changed example script for public repo | 18 May 2016, 21:53:42 UTC |
| a7ed3fe | timchu90 | 18 May 2016, 18:52:00 UTC | removed 'blah' file | 18 May 2016, 18:52:00 UTC |
| 28a9ee6 | timchu90 | 18 May 2016, 18:50:17 UTC | Merge branch 'varcall_filter-refactor' | 18 May 2016, 18:50:17 UTC |
| da5a3f2 | timchu90 | 18 May 2016, 18:49:51 UTC | clarified readme in machine learning step | 18 May 2016, 18:49:51 UTC |
| be78f23 | timchu90 | 18 May 2016, 15:12:43 UTC | added argument to merge step to require naming of final file | 18 May 2016, 15:12:43 UTC |
| ffb3d7c | timchu90 | 17 May 2016, 19:45:47 UTC | readME fix | 17 May 2016, 19:45:47 UTC |
| ac03d9c | timchu90 | 17 May 2016, 14:57:38 UTC | update readme | 17 May 2016, 14:57:38 UTC |
| d432c20 | timchu90 | 15 April 2016, 22:32:03 UTC | added vcftype arg to machine learning scripts some bug fixes to ML code | 15 April 2016, 22:32:03 UTC |
| c7b90d3 | timchu90 | 14 April 2016, 16:51:00 UTC | removing old files | 14 April 2016, 16:51:00 UTC |
| f1ee13c | timchu90 | 14 April 2016, 16:50:12 UTC | python wrapper for machine learning half | 14 April 2016, 16:50:12 UTC |
| d5ecc47 | timchu90 | 13 April 2016, 19:40:15 UTC | merge scripts into helper. changes to exit subprocess if error a few variable naming changes | 13 April 2016, 19:40:15 UTC |
| 3e4e5fb | timchu90 | 12 April 2016, 21:16:58 UTC | added back maf_to_tobi_som_var_list.sh, combined pp_scripts into one file | 12 April 2016, 21:16:58 UTC |
| 0853bb1 | timchu90 | 12 April 2016, 19:01:47 UTC | edited readme for vcd-filter portion. | 12 April 2016, 19:01:47 UTC |
| 11e299f | timchu90 | 06 April 2016, 20:17:44 UTC | removed unused files | 06 April 2016, 20:17:44 UTC |
| cbfc3bc | timchu90 | 06 April 2016, 19:05:05 UTC | working varcallfilter refactor results match test outputs. | 06 April 2016, 19:05:05 UTC |
| a6918c5 | timchu90 | 06 April 2016, 14:13:53 UTC | filter implemented. still testing outputs | 06 April 2016, 14:13:53 UTC |
| a5f118c | timchu90 | 04 April 2016, 16:43:44 UTC | added vcfEffFirstLine.pl into pipeline | 04 April 2016, 16:43:44 UTC |
| 2ab38f1 | timchu90 | 04 April 2016, 15:34:04 UTC | Merge branch 'master' into varcall_filter-refactor | 04 April 2016, 15:34:04 UTC |
| c9b6771 | cjmadubata | 04 April 2016, 14:54:57 UTC | add varCall_filtering/scripts/vcfEffFirstLine.pl which keeps first annotation | 04 April 2016, 14:54:57 UTC |
| 2d1aa97 | timchu90 | 01 April 2016, 19:45:33 UTC | added error handling of arguments | 01 April 2016, 19:45:33 UTC |
| 9d136cc | timchu90 | 01 April 2016, 16:57:37 UTC | fixed snpsift bug. reworked output directories piping snpsift output into same file caused errors. [WORKING BUILD] | 01 April 2016, 16:57:37 UTC |
| c73e387 | timchu90 | 01 April 2016, 15:45:36 UTC | annotation working. 1 bug? snpSift complains: Fatal Error: Your vcf files must be sorted! despite the vcf input having been sorted. | 01 April 2016, 15:45:36 UTC |
| 52207f9 | timchu90 | 31 March 2016, 21:57:02 UTC | added last step of annotation. fixed bugs still testing vcf-sort | 31 March 2016, 21:57:02 UTC |
| 4547f29 | timchu90 | 30 March 2016, 21:44:58 UTC | variant annotation almost done missing dbNSFP step | 30 March 2016, 21:44:58 UTC |
| 57e3f89 | timchu90 | 30 March 2016, 14:33:26 UTC | Revert "Merge remote-tracking branch 'origin/cjm_dev' into varcall_filter-refactor" This reverts commit 382030199156456e9c9e01b539a5980d2b6d0f58, reversing changes made to 9a2b4b7cac0dd3a90400207e69a01f0d7eb344ab. | 30 March 2016, 14:33:26 UTC |
| 3820301 | timchu90 | 30 March 2016, 14:33:05 UTC | Merge remote-tracking branch 'origin/cjm_dev' into varcall_filter-refactor | 30 March 2016, 14:33:05 UTC |
| 9a2b4b7 | timchu90 | 29 March 2016, 20:27:01 UTC | reorganized output folders and auto cleans tmp vcf | 29 March 2016, 20:27:01 UTC |
| 8c27ac1 | timchu90 | 29 March 2016, 18:45:29 UTC | bam to vcf working | 29 March 2016, 18:45:29 UTC |
| f55a7aa | cjmadubata | 28 March 2016, 23:01:37 UTC | Merge branch 'dev.bam_input' into cjm_dev | 28 March 2016, 23:01:37 UTC |
| e4ff4b3 | cjmadubata | 28 March 2016, 22:53:37 UTC | add machine_learning/machine_learning.bam_input.missing_val.R | 28 March 2016, 22:53:37 UTC |
| 6ef4eff | cjmadubata | 28 March 2016, 22:00:12 UTC | add machine_learning/pre_processing_glioma.151230.R, meant for bam inputs, all features | 28 March 2016, 22:00:12 UTC |
| b8d8ea4 | cjmadubata | 28 March 2016, 21:58:43 UTC | readme describes .bam input based TOBI runs | 28 March 2016, 21:58:43 UTC |
| 3b832ba | timchu90 | 28 March 2016, 21:37:24 UTC | implemented config reading and file creation | 28 March 2016, 21:37:24 UTC |
| 43d6694 | cjmadubata | 28 March 2016, 21:26:33 UTC | Merge branch 'dev.bam_input' into dev | 28 March 2016, 21:26:33 UTC |
| f585ee5 | cjmadubata | 28 March 2016, 21:26:15 UTC | modified varCall_filtering/do_annotation_filtering.sh_TCGA_protected.sh | 28 March 2016, 21:26:15 UTC |
| 06d5b9d | cjmadubata | 28 March 2016, 21:21:03 UTC | changes to do_annotation_filtering.sh_TCGA_protected.sh and scripts/filter_indel_techn_biol.pediatric.R | 28 March 2016, 21:21:03 UTC |
| 7b3c171 | cjmadubata | 28 March 2016, 21:17:45 UTC | add varCall_filtering/merge_all_tsvs.bam_input.sh for merging from bam files | 28 March 2016, 21:17:45 UTC |
| 08db6f3 | cjmadubata | 28 March 2016, 18:20:08 UTC | confirmed that all scripts work on bam files | 28 March 2016, 18:20:08 UTC |
| df7f74e | cjmadubata | 28 March 2016, 16:19:55 UTC | modified debug options in varCall_filtering/run_pipeline.sh to gzip filtered TSV | 28 March 2016, 16:19:55 UTC |
| 3214332 | cjmadubata | 28 March 2016, 16:16:56 UTC | add varCall_filtering/{run_pipeline.sh,filter_indel_techn_biol.pediatric.R}; change case name in batch file; edit debug options | 28 March 2016, 16:16:56 UTC |
| dc08f70 | timchu90 | 28 March 2016, 14:43:25 UTC | resend | 28 March 2016, 14:43:25 UTC |
| a6dc0e3 | timchu90 | 25 March 2016, 21:35:10 UTC | began porting vcf code to python. not working yet. please don’t run | 25 March 2016, 21:35:10 UTC |
| 7096506 | cjmadubata | 25 March 2016, 20:41:38 UTC | add varCall_filtering/do_annotation_filtering.debug.bam.sh; replace batch_multi_array.bam_input.sh | 25 March 2016, 20:41:38 UTC |
| c216bba | cjmadubata | 24 March 2016, 15:29:12 UTC | removed conflicting header file | 24 March 2016, 15:29:12 UTC |
| 8130924 | timchu90 | 24 March 2016, 15:26:34 UTC | Merge branch 'master' into varcall_filter-refactor | 24 March 2016, 15:26:34 UTC |
| 8b17471 | cjmadubata | 24 March 2016, 15:25:03 UTC | add varCall_filtering/scripts/header_fields.txt, was removed at 26b6ab5 | 24 March 2016, 15:25:03 UTC |
| e13cf4b | cjmadubata | 24 March 2016, 15:19:49 UTC | add varCall_filtering/batch_multi_array.bam_input.sh | 24 March 2016, 15:19:49 UTC |
| 26b6ab5 | cjmadubata | 24 March 2016, 14:27:54 UTC | rename varCall_filtering/scripts/old.header_fields.txt to header_fields.txt | 24 March 2016, 14:27:54 UTC |
| 858137d | timchu90 | 24 March 2016, 14:27:03 UTC | publish refactor branch | 24 March 2016, 14:27:03 UTC |
| b3f67ae | cjmadubata | 24 March 2016, 13:56:56 UTC | rename machine_learning/ml_scripts/na_minus1.R to na_to_mean.R, improve descr. | 24 March 2016, 13:56:56 UTC |
| b3a8b8b | cjmadubata | 24 March 2016, 00:00:38 UTC | delete machine_learning/old.ml_scripts/ | 24 March 2016, 00:00:38 UTC |
| d1d257b | cjmadubata | 23 March 2016, 23:57:45 UTC | add total time pre_processing.R; readme.txt moved ar3177 git path | 23 March 2016, 23:57:45 UTC |
| 3ce929e | cjmadubata | 23 March 2016, 23:30:15 UTC | move ml_scripts/ to old.ml_scripts/, na_minus1/ to ml_scripts/ | 23 March 2016, 23:30:15 UTC |
| b4d77d4 | cjmadubata | 23 March 2016, 23:23:50 UTC | clean paths in machine_learning_broad.missing_val.R | 23 March 2016, 23:23:50 UTC |
| fd7e248 | cjmadubata | 23 March 2016, 19:48:44 UTC | add myPerf.y_col_name_not_obs.R top_pred.all_genes.ROC_function.R to na_minus1 | 23 March 2016, 19:48:44 UTC |
| 2448aec | cjmadubata | 23 March 2016, 19:42:20 UTC | add machine_learning/na_minus1/ | 23 March 2016, 19:42:20 UTC |
| 4c57000 | cjmadubata | 23 March 2016, 19:36:11 UTC | add machine_learning/pre_processing.R, mv old ml/files | 23 March 2016, 19:36:11 UTC |
| cd5cfe8 | cjmadubata | 23 March 2016, 19:22:17 UTC | added filter_indel_techn_biol.LGG_TCGA_protect.R | 23 March 2016, 19:22:17 UTC |
| 9a2b031 | cjmadubata | 23 March 2016, 19:20:32 UTC | added TCGA vcf2report | 23 March 2016, 19:20:32 UTC |
| 13c96bf | cjmadubata | 23 March 2016, 19:03:06 UTC | note sed -i '1s/cnt/cosmic_nsamp/' | 23 March 2016, 19:03:06 UTC |
| acf8a98 | cjmadubata | 23 March 2016, 18:59:17 UTC | add varCall_filtering/merge_all_tsvs.sh, note use in readme.txt | 23 March 2016, 18:59:17 UTC |
| df9cf71 | cjmadubata | 23 March 2016, 18:53:56 UTC | add varCall_filtering/tobi_out_empty.sh, note usage in readme.txt | 23 March 2016, 18:53:56 UTC |
| 7dc31e4 | cjmadubata | 23 March 2016, 18:47:29 UTC | readme describes how to use TOBI through vcf var call and filter | 23 March 2016, 18:47:29 UTC |
| 9a5d386 | cjmadubata | 23 March 2016, 18:37:50 UTC | add varCall_filtering/maf_to_tobi_som_var_list.sh, note in readme | 23 March 2016, 18:37:50 UTC |
| a5fad73 | cjmadubata | 23 March 2016, 16:58:06 UTC | move all old .sh files in varCall* to old*sh | 23 March 2016, 16:58:06 UTC |
| 61144ee | cjmadubata | 23 March 2016, 16:55:26 UTC | add note to readme | 23 March 2016, 16:55:26 UTC |
| 47c9253 | cjmadubata | 23 March 2016, 16:53:48 UTC | add note to readme that TCGA VCF | 23 March 2016, 16:53:48 UTC |
| c66e0ea | ar3177 | 09 January 2015, 23:00:43 UTC | - Minor bug fixes. | 09 January 2015, 23:00:43 UTC |
| 1ce5c70 | ar3177 | 19 December 2014, 20:05:52 UTC | - Minor bug fixes. Added Recur feature, but it's not used at the time. | 19 December 2014, 20:05:52 UTC |
| 8924796 | ar3177 | 18 November 2014, 17:05:47 UTC | - Included necessary data for preprocessing in the pipeline. | 18 November 2014, 17:05:47 UTC |
| c8105f8 | ar3177 | 13 November 2014, 17:29:52 UTC | - Changed gbm_pipeline folder name to varCall_filtering. | 13 November 2014, 17:29:52 UTC |
| f2cfb48 | ar3177 | 12 November 2014, 23:14:58 UTC | - Added filter flag. | 12 November 2014, 23:14:58 UTC |
| 2832409 | ar3177 | 12 November 2014, 21:58:00 UTC | - Added flags to batch_multi_array. It can be run from the command line now. | 12 November 2014, 21:58:00 UTC |
| 529baa9 | ar3177 | 12 November 2014, 21:10:44 UTC | - Bug fix | 12 November 2014, 21:10:44 UTC |
| 068346f | ar3177 | 12 November 2014, 19:51:38 UTC | - Minor corrections to batch_multi_array. | 12 November 2014, 19:51:38 UTC |
| a6d6ab8 | ar3177 | 11 November 2014, 21:14:20 UTC | - Edited batch_multi_array to automatically detect if it is on HPC or on Amazon | 11 November 2014, 21:14:20 UTC |
| 1dbdcbb | ar3177 | 11 November 2014, 20:48:45 UTC | - Edited readme | 11 November 2014, 20:48:45 UTC |
| 463adbb | ar3177 | 07 November 2014, 21:18:13 UTC | - readme.txt moved. | 07 November 2014, 21:18:13 UTC |
| 8343dd1 | ar3177 | 07 November 2014, 21:16:23 UTC | - Moved readme.txt file to the main folder. | 07 November 2014, 21:16:23 UTC |
| e5fd1a1 | ar3177 | 07 November 2014, 21:09:48 UTC | - Added tobi_config files for hpc and amazon. Moved hard-wired links to config files. Added Readme file. Removed batch_multi_sample.sh. | 07 November 2014, 21:09:48 UTC |
| 9daf755 | ar3177 | 07 November 2014, 16:52:03 UTC | - Removed .DS_Store files. Added pfam_cosmic_fun.R | 07 November 2014, 16:52:03 UTC |
| cb9b15b | ar3177 | 07 October 2014, 16:04:08 UTC | - Modularized pre_preprocessing, and moved the cleaning from machine_learning to there | 07 October 2014, 16:04:08 UTC |
| d296926 | ar3177 | 06 October 2014, 21:13:07 UTC | - Added indels to the machine learning step. The feature can be turned on and off. | 06 October 2014, 21:13:07 UTC |
| a5e0fa9 | ar3177 | 02 October 2014, 17:58:31 UTC | - Removed the moved files from machine_learning/scripts | 02 October 2014, 17:58:31 UTC |
| 900f041 | ar3177 | 02 October 2014, 17:52:03 UTC | - Moved ML scripts to a dedicated folder - Created pp_scripts folder and moved all the post-processing scripts there | 02 October 2014, 17:52:03 UTC |
