| e48195c | rernst | 08 May 2015, 08:47:47 UTC | Merge branch 'release-v1.2.2' | 08 May 2015, 08:47:47 UTC |
| 9c07ce7 | rernst | 08 May 2015, 08:46:10 UTC | Improve error message | 08 May 2015, 08:46:10 UTC |
| 95bd82f | rernst | 08 May 2015, 08:34:54 UTC | Update ini files | 08 May 2015, 08:34:54 UTC |
| 1c9f06d | rernst | 08 May 2015, 08:34:35 UTC | Store strelka ini files in IAP settings dir | 08 May 2015, 08:34:35 UTC |
| 5ab3b6d | rernst | 06 May 2015, 12:04:50 UTC | Update CPCT somatic variant sample name regex | 06 May 2015, 12:04:50 UTC |
| e5d3c0c | rernst | 05 May 2015, 11:26:44 UTC | Update snpeff to v4.1e | 05 May 2015, 11:26:44 UTC |
| aa8726b | rernst | 29 April 2015, 10:30:53 UTC | Add flagstat settings | 29 April 2015, 10:30:53 UTC |
| 05a375a | rernst | 29 April 2015, 09:18:34 UTC | Update FastQC to v0.11.3, solves threading bug | 29 April 2015, 09:18:34 UTC |
| 01b6e2e | rernst | 29 April 2015, 09:17:18 UTC | Print input fail message to stdout | 29 April 2015, 09:17:18 UTC |
| fa7e3b0 | rernst | 28 April 2015, 09:26:28 UTC | Merge branch 'develop' of github.com:CuppenResearch/IAP into develop | 28 April 2015, 09:26:28 UTC |
| faa8fb0 | rernst | 28 April 2015, 09:25:03 UTC | Skip merge for single lane/bam samples, for now rerun index/flagstat. Solves: #11 | 28 April 2015, 09:25:03 UTC |
| 40421c0 | rernst | 28 April 2015, 08:20:15 UTC | print all warnings to stdout | 28 April 2015, 08:20:15 UTC |
| 4010e22 | Robert Ernst | 24 April 2015, 09:06:05 UTC | Update README.md | 24 April 2015, 09:06:05 UTC |
| 3e4eb5f | Robert Ernst | 24 April 2015, 08:47:46 UTC | Update README.md | 24 April 2015, 08:47:46 UTC |
| 9d7b363 | rernst | 24 April 2015, 07:52:28 UTC | Add -R to qsub for poststats and prestats | 24 April 2015, 07:52:28 UTC |
| b7dfef1 | rernst | 23 April 2015, 14:22:55 UTC | Fix realign log, solves #10 | 23 April 2015, 14:22:55 UTC |
| 319ac9e | rernst | 15 April 2015, 12:47:53 UTC | Added check and continue control for each mapping step | 15 April 2015, 12:47:53 UTC |
| 2e52520 | rernst | 15 April 2015, 12:46:43 UTC | Improved error message for poststats | 15 April 2015, 12:46:43 UTC |
| 0c26285 | rernst | 13 April 2015, 11:57:56 UTC | Remove mainjob.sh and use system command to start realign jobs | 13 April 2015, 11:57:56 UTC |
| ec667a5 | rernst | 13 April 2015, 10:34:28 UTC | Add separate jobs and settings for Flagstats | 13 April 2015, 10:34:52 UTC |
| 2eb5fbf | rernst | 13 April 2015, 07:27:47 UTC | Add --tmpdir option to sambamba jobs | 13 April 2015, 07:27:47 UTC |
| 7fd6387 | rernst | 10 April 2015, 10:16:56 UTC | Merge branch 'release-v1.2.1' into develop | 10 April 2015, 10:16:56 UTC |
| 29807d0 | rernst | 10 April 2015, 10:11:37 UTC | Merge branch 'release-v1.2.1' | 10 April 2015, 10:11:37 UTC |
| b0b7013 | rernst | 10 April 2015, 08:55:05 UTC | Update and new ini files | 10 April 2015, 08:55:05 UTC |
| dd06318 | rernst | 09 April 2015, 13:59:51 UTC | Consistent .err and .out paths for poststats jobs | 09 April 2015, 13:59:51 UTC |
| 7a8e9f0 | rernst | 09 April 2015, 13:40:23 UTC | Seperate jobs for BQSR flagstat | 09 April 2015, 13:40:23 UTC |
| aa5d18e | rernst | 09 April 2015, 13:38:38 UTC | Add scatters back to genotypeGVCF | 09 April 2015, 13:38:38 UTC |
| 90521cf | rernst | 07 April 2015, 07:12:41 UTC | Add check for ref sample when running illumina check and somatic jobs | 07 April 2015, 07:12:41 UTC |
| 6538911 | rernst | 02 April 2015, 07:40:49 UTC | Change sample working bam before skipping recal step. | 02 April 2015, 07:40:49 UTC |
| bc60171 | rernst | 01 April 2015, 11:12:08 UTC | HPC Bug: poststats now generates seperate log files per job per sample | 01 April 2015, 11:12:08 UTC |
| 4bc70bd | rernst | 27 March 2015, 13:42:25 UTC | Remove scatters from genotypeGVCFs command | 27 March 2015, 13:42:25 UTC |
| 5927cc8 | rernst | 20 March 2015, 14:19:11 UTC | Set queue calling job memory | 20 March 2015, 14:19:11 UTC |
| 432c03b | rernst | 20 March 2015, 14:18:30 UTC | Update genome ini files | 20 March 2015, 14:18:30 UTC |
| 425c7df | rernst | 20 March 2015, 11:51:41 UTC | Update and add ini files | 20 March 2015, 11:51:41 UTC |
| bc2520c | rernst | 20 March 2015, 11:29:40 UTC | Add scatter and nct to genotypeGVCFs | 20 March 2015, 11:29:40 UTC |
| 4e063ef | rernst | 19 March 2015, 12:57:29 UTC | Check and/or symlink flagstat and bai for bam input | 19 March 2015, 12:57:29 UTC |
| 344342a | rernst | 12 March 2015, 12:00:03 UTC | Merge branch 'release-v1.2.0' into develop | 12 March 2015, 12:00:03 UTC |
| c555ef0 | rernst | 12 March 2015, 11:58:08 UTC | Merge branch 'release-v1.2.0' | 12 March 2015, 11:58:08 UTC |
| a36a2fc | rernst | 12 March 2015, 09:40:45 UTC | Two new ini files | 12 March 2015, 09:40:45 UTC |
| 67a6187 | rernst | 12 March 2015, 09:31:01 UTC | Rollback Freebayes update | 12 March 2015, 09:31:01 UTC |
| 6bce116 | rernst | 10 March 2015, 14:32:16 UTC | Update Freebayes and increase queue | 10 March 2015, 14:32:16 UTC |
| d06c8c3 | rernst | 10 March 2015, 14:27:45 UTC | Update ini files to work with CNV analysis | 10 March 2015, 14:27:45 UTC |
| a3397e9 | rernst | 09 March 2015, 12:58:59 UTC | Merge branch 'copynumber-v1.2' into develop | 09 March 2015, 12:58:59 UTC |
| 1f1afda | rernst | 09 March 2015, 10:30:26 UTC | Move config check to illumina_pipeline.pl and remove from the modules | 09 March 2015, 10:30:26 UTC |
| d99a16c | rernst | 06 March 2015, 14:10:57 UTC | Move config checks to illumina_pipeline.pl | 06 March 2015, 14:10:57 UTC |
| e6b80bc | rernst | 06 March 2015, 09:26:19 UTC | Add CNV option check | 06 March 2015, 09:26:19 UTC |
| 8f7d778 | rernst | 05 March 2015, 15:10:01 UTC | Rename copynumber to copyNumber | 05 March 2015, 15:10:01 UTC |
| ecf1ee3 | rernst | 05 March 2015, 15:01:16 UTC | Add copynumber support | 05 March 2015, 15:01:16 UTC |
| 7c724ee | rernst | 03 March 2015, 09:09:52 UTC | Merge branch 'release-v1.1.2' into develop | 03 March 2015, 09:09:52 UTC |
| 5ed5e8e | rernst | 03 March 2015, 09:05:43 UTC | Merge branch 'release-v1.1.2' | 03 March 2015, 09:05:43 UTC |
| c4d99e8 | rernst | 03 March 2015, 09:04:58 UTC | Bugfix varscan check | 03 March 2015, 09:04:58 UTC |
| c6cd5e5 | rernst | 03 March 2015, 08:02:27 UTC | Check varscan and freebayes final output files | 03 March 2015, 08:02:27 UTC |
| 77f393c | rernst | 26 February 2015, 14:18:56 UTC | Clean ini file | 26 February 2015, 14:18:56 UTC |
| b56b08c | rernst | 26 February 2015, 12:19:08 UTC | Update to dbnsfp 2.9 | 26 February 2015, 12:19:08 UTC |
| 9b7da4d | rernst | 26 February 2015, 11:59:33 UTC | Add more checks before and after running somatic caller jobs | 26 February 2015, 11:59:33 UTC |
| bbbccdf | rernst | 26 February 2015, 11:58:52 UTC | add samtools_path to ini | 26 February 2015, 11:58:52 UTC |
| f101af8 | rernst | 24 February 2015, 11:29:52 UTC | Add pileup pipe to varscan | 24 February 2015, 11:29:52 UTC |
| a7a0cc0 | rernst | 23 February 2015, 13:12:16 UTC | Check correct somatic sample name | 23 February 2015, 13:12:16 UTC |
| ad26c59 | rernst | 23 February 2015, 12:08:50 UTC | Check sample ref | 23 February 2015, 12:08:50 UTC |
| aa2e522 | rernst | 17 February 2015, 10:14:21 UTC | Update to snpeff v4.1b | 17 February 2015, 10:14:21 UTC |
| 364db49 | rernst | 16 February 2015, 13:06:27 UTC | Rename SOMATIC_TARGETS to SOMVAR_TARGETS and change ini file | 16 February 2015, 13:06:27 UTC |
| 5e1b1fb | rernst | 16 February 2015, 12:55:40 UTC | Add SOMATIC_TARGETS and filter on targets | 16 February 2015, 12:55:40 UTC |
| 30e63e6 | rernst | 16 February 2015, 08:29:35 UTC | Move .pdf report after realignment | 16 February 2015, 08:29:35 UTC |
| 292a8b5 | rernst | 11 February 2015, 14:41:57 UTC | Map lanes to bam.tmp and mv when done | 11 February 2015, 14:41:57 UTC |
| de3b1ae | rernst | 06 February 2015, 11:41:50 UTC | Merge branch 'gVCF-v1.2' into develop | 06 February 2015, 11:41:50 UTC |
| 9d14060 | rernst | 06 February 2015, 11:41:10 UTC | Add CALLING_GVCF to ini files | 06 February 2015, 11:41:10 UTC |
| b63de3c | rernst | 03 February 2015, 14:46:34 UTC | Output gvcf as vcf.gz | 03 February 2015, 14:46:34 UTC |
| 9e33900 | rernst | 03 February 2015, 13:54:23 UTC | gVCF scala script | 03 February 2015, 13:54:23 UTC |
| e7f3d45 | rernst | 03 February 2015, 13:53:01 UTC | Add gvcf support | 03 February 2015, 13:53:01 UTC |
| a58f66d | rernst | 03 February 2015, 10:01:30 UTC | Add -t to fastqc | 03 February 2015, 10:01:30 UTC |
| 7a3e520 | rernst | 03 February 2015, 09:31:32 UTC | Merge branch 'hotfix-v1.1.1' into develop | 03 February 2015, 09:31:32 UTC |
| 8edf43f | rernst | 03 February 2015, 09:26:38 UTC | Merge branch 'hotfix-v1.1.1' | 03 February 2015, 09:26:38 UTC |
| 8e7438f | rernst | 03 February 2015, 08:58:55 UTC | Fix strelka GT field regex | 03 February 2015, 08:58:55 UTC |
| eacc2d8 | rernst | 29 January 2015, 13:49:58 UTC | Update to dbNSFP v2.8 | 29 January 2015, 13:49:58 UTC |
| 2dcd12e | rernst | 29 January 2015, 13:40:45 UTC | Add igvtools to ini | 29 January 2015, 13:40:45 UTC |
| 2ed51cc | rernst | 29 January 2015, 13:32:25 UTC | chmod | 29 January 2015, 13:32:25 UTC |
| f093ebb | rernst | 29 January 2015, 13:31:43 UTC | Update settings | 29 January 2015, 13:31:43 UTC |
| e37f11d | rernst | 29 January 2015, 13:28:14 UTC | Rename ini file | 29 January 2015, 13:28:14 UTC |
| 644e08c | rernst | 29 January 2015, 13:16:12 UTC | Added GT fields to strelka calls for gatk compatibility | 29 January 2015, 13:16:12 UTC |
| 71394d8 | rernst | 29 January 2015, 09:21:23 UTC | Add igvtools index step | 29 January 2015, 09:21:23 UTC |
| 528d30d | rernst | 28 January 2015, 12:00:36 UTC | Remove .idx of deleted vcf files and create index after SnpSift annotation | 28 January 2015, 12:00:36 UTC |
| b3643aa | rernst | 28 January 2015, 11:57:33 UTC | Fix merging somatic vcf | 28 January 2015, 11:57:33 UTC |
| a5b8161 | rernst | 23 January 2015, 12:55:20 UTC | Merge branch 'release-v1.1' into develop | 23 January 2015, 12:55:20 UTC |
| ac4301f | rernst | 23 January 2015, 12:54:27 UTC | Merge branch 'release-v1.1' | 23 January 2015, 12:54:27 UTC |
| 8a66caa | rernst | 23 January 2015, 12:01:16 UTC | Add SOMATIC_VARIANTS option to ini files | 23 January 2015, 12:01:16 UTC |
| 84d2d26 | rernst | 23 January 2015, 11:50:55 UTC | Merge branch 'SomaticVariant-v1.1' into develop | 23 January 2015, 11:50:55 UTC |
| b4c2f3c | rernst | 23 January 2015, 10:21:48 UTC | Add reserve tag and change order of annotations to 'fix' gatk bug | 23 January 2015, 11:45:49 UTC |
| 1f1c429 | rernst | 23 January 2015, 10:21:01 UTC | Fix error message | 23 January 2015, 11:45:49 UTC |
| fa6072b | rernst | 23 January 2015, 09:45:35 UTC | Increase annotation threads | 23 January 2015, 11:45:49 UTC |
| 368e4ea | rernst | 23 January 2015, 09:16:56 UTC | Remove empty log files | 23 January 2015, 11:45:48 UTC |
| e6ccdf4 | rernst | 22 January 2015, 13:49:15 UTC | Add ANNOTATE_ID settings to ini files | 23 January 2015, 11:45:48 UTC |
| 71ce3d7 | rernst | 22 January 2015, 13:47:52 UTC | Add ANNOTATE_ID to be used for annotating vcfs with for example cosmic ids | 23 January 2015, 11:45:48 UTC |
| c217beb | rernst | 22 January 2015, 12:40:23 UTC | Add reserve flag | 23 January 2015, 11:45:47 UTC |
| 539c617 | rernst | 22 January 2015, 11:28:55 UTC | Fixed missing setting warning and updated settings | 23 January 2015, 11:45:47 UTC |
| f185172 | rernst | 22 January 2015, 07:56:28 UTC | Rename somatic ini file | 23 January 2015, 11:45:47 UTC |
| b617c2c | rernst | 21 January 2015, 08:57:47 UTC | Update cpct_name regex | 23 January 2015, 11:45:47 UTC |
| e383bef | rernst | 16 January 2015, 13:18:16 UTC | Add somatic variant callers to final check script | 23 January 2015, 11:45:46 UTC |
| d91e0de | rernst | 17 December 2014, 12:16:23 UTC | Check for undef jobs and .done file | 23 January 2015, 11:45:46 UTC |
| ff8ad06 | rernst | 17 December 2014, 11:23:48 UTC | Added somaticvariants merge job and checks for ini/conf files | 23 January 2015, 11:45:46 UTC |
| 3c4e314 | rernst | 16 December 2014, 10:10:04 UTC | Removed redundant steps and started with final merged vcf file | 23 January 2015, 11:45:45 UTC |
