| f73ff31 | Robert Ernst | 03 April 2020, 13:56:36 UTC | Fix tabs | 03 April 2020, 13:56:36 UTC |
| ccd93ed | Martin Elferink | 05 March 2020, 07:25:07 UTC | Merge pull request #122 from UMCUGenetics/IAP_ExomeDepth Iap exomedepth | 05 March 2020, 07:25:07 UTC |
| 8c698dc | melferink | 04 March 2020, 11:40:27 UTC | fixed bash check | 04 March 2020, 11:40:27 UTC |
| ccac8d2 | melferink | 03 March 2020, 06:44:39 UTC | clarification | 03 March 2020, 06:44:39 UTC |
| b32af22 | melferink | 02 March 2020, 12:22:19 UTC | included ExomeDepth | 02 March 2020, 12:22:19 UTC |
| 0c2f742 | melferink | 02 March 2020, 09:14:02 UTC | added ExomeDepth checking | 02 March 2020, 09:14:02 UTC |
| a25127f | melferink | 02 March 2020, 07:01:16 UTC | added code for Exomedepth | 02 March 2020, 07:01:16 UTC |
| d14fe1e | rernst | 08 April 2019, 08:10:10 UTC | Add temp directory | 08 April 2019, 08:10:10 UTC |
| 484f61f | rernst | 25 March 2019, 10:32:54 UTC | Improve exoncov v3 check | 25 March 2019, 13:44:25 UTC |
| b360a31 | rernst | 21 March 2019, 14:16:07 UTC | Add overwrite to exoncov v3 command | 21 March 2019, 14:16:07 UTC |
| 642c6d5 | rernst | 19 March 2019, 15:38:45 UTC | Add exon_bed and threads | 19 March 2019, 15:38:45 UTC |
| 371763c | rernst | 14 March 2019, 14:42:58 UTC | Temporary add EXONCOVV3 | 15 March 2019, 14:58:37 UTC |
| 74a37ba | Joep de Ligt | 02 October 2018, 13:09:08 UTC | Merge pull request #118 from FreekManders/develop Small fix to BAF plot | 02 October 2018, 13:09:08 UTC |
| 461ebbf | FreekManders | 02 October 2018, 08:35:23 UTC | Made a small fix to the indexing of the bins for the BAF plot. The bins were too large, because R indexing is inclusive. The too large bins resulted in some variants being present in three bins. | 02 October 2018, 08:35:23 UTC |
| d3ef138 | Robert Ernst | 01 November 2017, 14:51:15 UTC | Merge pull request #114 from UMCUGenetics/gatk_3.8 Gatk 3.8 | 01 November 2017, 14:51:15 UTC |
| 34d1314 | rernst | 01 November 2017, 14:50:20 UTC | update ini and readme | 01 November 2017, 14:50:20 UTC |
| b4da87a | rernst | 02 October 2017, 08:06:26 UTC | Remove stand emit conf from gvcf route | 01 November 2017, 14:00:09 UTC |
| 6346ef3 | rernst | 29 September 2017, 11:07:18 UTC | Update ini's with gatk 3.8 | 01 November 2017, 14:00:09 UTC |
| 815e15e | rernst | 03 March 2017, 15:29:47 UTC | Update Readme | 01 November 2017, 14:00:09 UTC |
| 67b9340 | rernst | 03 March 2017, 15:17:36 UTC | Update ini with new settings | 01 November 2017, 14:00:08 UTC |
| 9544e19 | rernst | 03 March 2017, 14:59:06 UTC | Add GATK Java module | 01 November 2017, 13:59:15 UTC |
| 966d21a | rernst | 02 March 2017, 08:46:11 UTC | Add gatk3.7 calling settings to ini check. | 01 November 2017, 13:59:14 UTC |
| ceaf682 | rernst | 01 March 2017, 10:14:04 UTC | Make scala script compatible with gatk 3.7 | 01 November 2017, 13:59:14 UTC |
| 63069af | Robert Ernst | 01 November 2017, 13:57:45 UTC | Merge pull request #112 from UMCUGenetics/hartwig_3 Hartwig 3 | 01 November 2017, 13:57:45 UTC |
| db1ef35 | rernst | 01 November 2017, 09:16:00 UTC | Use only hmftools versioning. | 01 November 2017, 09:16:00 UTC |
| 6e1946a | rernst | 05 October 2017, 12:15:29 UTC | Hartwig v3 somatic snv and sv changes | 11 October 2017, 13:01:17 UTC |
| 4e7e088 | rernst | 22 September 2017, 11:29:51 UTC | Check if input_vcf exists before starting single sample vcf step. | 22 September 2017, 11:29:51 UTC |
| 6c35bba | rernst | 26 July 2017, 09:27:08 UTC | Make Base Recalibration QC optional. | 26 July 2017, 09:27:08 UTC |
| c216945 | rernst | 19 June 2017, 13:22:59 UTC | Add CHECKING_CLEANUP step | 19 June 2017, 13:22:59 UTC |
| 42c56d1 | rernst | 19 June 2017, 09:00:22 UTC | Add stand_emit_conf and stand_call_conf to genotype gvcf step. | 19 June 2017, 09:00:22 UTC |
| cb913e2 | Robert Ernst | 07 April 2017, 11:21:35 UTC | Update README.md Add DOI. | 07 April 2017, 11:21:35 UTC |
| 346b1b6 | rernst | 07 April 2017, 10:57:38 UTC | Merge branch 'release-v2.6.0' into develop | 07 April 2017, 10:57:38 UTC |
| 8d30ad1 | rernst | 06 April 2017, 13:15:45 UTC | Ini: Remove tab from EXONCALLCOV_MEM setting | 06 April 2017, 13:15:45 UTC |
| 4c3e27b | rernst | 28 March 2017, 14:06:37 UTC | Add id from design to variant calls. | 28 March 2017, 14:06:37 UTC |
| d364fbe | rernst | 28 March 2017, 11:19:03 UTC | Fix #104. | 28 March 2017, 11:19:03 UTC |
| ef12025 | rernst | 28 March 2017, 09:08:43 UTC | Fix #96. | 28 March 2017, 09:08:43 UTC |
| 99800e4 | rernst | 28 March 2017, 09:07:14 UTC | Fix #84. | 28 March 2017, 09:07:14 UTC |
| d472f86 | rernst | 24 March 2017, 12:04:12 UTC | Update bcftools to fix roh analysis. Solves #103. | 24 March 2017, 12:04:12 UTC |
| 5404049 | Robert Ernst | 23 March 2017, 13:20:06 UTC | Merge pull request #102 from UMCUGenetics/hmf1.12 Hartwig IAP 1.12 changes | 23 March 2017, 13:20:06 UTC |
| 53a36f4 | rernst | 21 March 2017, 13:57:06 UTC | Merge branch 'develop' of github.com:CuppenResearch/IAP into develop | 21 March 2017, 13:57:06 UTC |
| 7865bf0 | rernst | 21 March 2017, 13:56:43 UTC | Change EXONCALLCOV track location | 21 March 2017, 13:56:43 UTC |
| 1f075b2 | rernst | 13 March 2017, 15:19:01 UTC | Freec changes, #99. | 13 March 2017, 15:19:01 UTC |
| 3343148 | rernst | 13 March 2017, 12:27:43 UTC | Somatic changes, #99 | 13 March 2017, 12:27:43 UTC |
| f18c52e | mroosmalen | 09 March 2017, 09:41:06 UTC | Add INS calling for DELLY, fix #101 | 09 March 2017, 09:41:06 UTC |
| 8651000 | rernst | 07 March 2017, 10:13:43 UTC | Add SOMATIC_REGEX_REF_CODE and SOMATIC_REGEX_TUMOR_CODE settings to make tumor/ref parsing more versatile. | 07 March 2017, 10:17:36 UTC |
| 29660bf | rernst | 10 February 2017, 12:08:48 UTC | Make sure indel and snp filters have unique names | 10 February 2017, 12:08:48 UTC |
| 463b64b | rernst | 03 February 2017, 09:51:08 UTC | Merge branch 'release-v2.5.0' into develop | 03 February 2017, 09:51:08 UTC |
| acc499b | rernst | 30 January 2017, 09:14:30 UTC | Update Dx_resources path | 30 January 2017, 09:14:30 UTC |
| 4ed69d5 | rernst | 27 January 2017, 13:04:31 UTC | Typo fix | 27 January 2017, 13:04:31 UTC |
| e150f40 | rernst | 26 January 2017, 12:05:10 UTC | Remove space from ini file | 26 January 2017, 12:05:10 UTC |
| 8e91c91 | rernst | 26 January 2017, 12:02:52 UTC | Allow only one mappability track in freec analysis | 26 January 2017, 12:02:52 UTC |
| 2438f83 | rernst | 25 January 2017, 09:29:12 UTC | Add --temporary-directory to vcf-sort in delly analysis, fix #95 | 25 January 2017, 09:29:12 UTC |
| 8035fa0 | rernst | 25 January 2017, 09:24:27 UTC | Update ini | 25 January 2017, 09:24:27 UTC |
| 7f4a702 | Robert Ernst | 19 January 2017, 09:20:16 UTC | Merge pull request #92 from CuppenResearch/feature-hartwig_v1.10-11_changes Hartwig v1.10-11 changes | 19 January 2017, 09:20:16 UTC |
| cd73f31 | rernst | 17 January 2017, 15:27:20 UTC | Decrease varscan threads | 17 January 2017, 15:27:20 UTC |
| 106e967 | rernst | 17 January 2017, 12:12:05 UTC | Move ROH output to roh folder | 17 January 2017, 12:12:05 UTC |
| 1df8926 | rernst | 17 January 2017, 11:40:21 UTC | Update ini files | 17 January 2017, 11:40:21 UTC |
| 2c08f14 | rernst | 17 January 2017, 11:40:11 UTC | Add single sample vcf step to vcfutils. | 17 January 2017, 11:40:11 UTC |
| 2ceee65 | Robert Ernst | 12 January 2017, 15:00:23 UTC | Merge pull request #93 from CuppenResearch/feature_snpPanel Feature Fingerprint | 12 January 2017, 15:00:23 UTC |
| c168761 | rernst | 12 January 2017, 11:17:58 UTC | Add fingerprint settings | 12 January 2017, 11:17:58 UTC |
| 5d982a9 | rernst | 12 January 2017, 11:16:58 UTC | Rename SNPPanel to fingerprint | 12 January 2017, 11:16:58 UTC |
| 74e9515 | rernst | 11 January 2017, 16:42:57 UTC | New SNP Panel calling analysis | 11 January 2017, 16:42:57 UTC |
| 3617a40 | rernst | 10 January 2017, 13:50:29 UTC | remove debug print | 10 January 2017, 13:50:29 UTC |
| 309bd97 | rernst | 10 January 2017, 12:43:11 UTC | Check fastq.gz pattern | 10 January 2017, 12:43:11 UTC |
| bf59b75 | rernst | 09 January 2017, 14:23:57 UTC | Move vt normalize to chr steps | 09 January 2017, 14:23:57 UTC |
| 4268395 | rernst | 09 January 2017, 14:20:13 UTC | Update melt script | 09 January 2017, 14:20:13 UTC |
| 698b993 | rernst | 06 January 2017, 13:50:51 UTC | PEP8 cleanup | 06 January 2017, 13:50:51 UTC |
| f47f963 | rernst | 06 January 2017, 13:42:40 UTC | Update filterFreebayes script | 06 January 2017, 13:42:40 UTC |
| dc5d12f | rernst | 06 January 2017, 12:27:24 UTC | Add version to vcflib path | 06 January 2017, 12:27:24 UTC |
| 1f037a3 | rernst | 06 January 2017, 10:32:26 UTC | Use human readable --min-alternate-count setting | 06 January 2017, 10:32:26 UTC |
| 8dbf380 | rernst | 05 January 2017, 13:45:17 UTC | Add VT normalize to freebayes analysis | 05 January 2017, 13:45:17 UTC |
| 5ca3882 | Robert Ernst | 05 January 2017, 13:19:05 UTC | update varscan settings | 05 January 2017, 13:19:05 UTC |
| 11a5a7b | Robert Ernst | 05 January 2017, 09:25:07 UTC | Cleanup python code | 05 January 2017, 09:25:07 UTC |
| 68eded4 | rernst | 05 January 2017, 09:04:41 UTC | Initial implementation of bcftools roh | 05 January 2017, 09:04:41 UTC |
| b64b2ae | Robert Ernst | 13 December 2016, 12:37:20 UTC | Merge pull request #90 from CuppenResearch/feature_namespace Feature namespace | 13 December 2016, 12:37:20 UTC |
| e1c3336 | Robert Ernst | 18 November 2016, 09:31:00 UTC | Merge pull request #88 from roelj/develop Put perl modules in their own namespace. | 18 November 2016, 09:31:00 UTC |
| 0c08d5a | Roel Janssen | 16 November 2016, 08:39:57 UTC | Put perl modules in their own namespace. | 16 November 2016, 08:39:57 UTC |
| 2006859 | rernst | 11 November 2016, 13:56:09 UTC | Add recalibrated bams to checking_rm list | 11 November 2016, 13:56:09 UTC |
| e6ead5a | rernst | 07 November 2016, 09:07:23 UTC | Change default opengrid group | 07 November 2016, 09:07:23 UTC |
| 4f3f2a7 | rernst | 02 November 2016, 14:26:47 UTC | Merge branch 'release-v2.4.0' into develop | 02 November 2016, 14:26:47 UTC |
| a2c05b7 | rernst | 02 November 2016, 14:24:29 UTC | Update ini | 02 November 2016, 14:24:29 UTC |
| 94522bd | rernst | 02 November 2016, 09:20:30 UTC | Update ini | 02 November 2016, 09:20:30 UTC |
| 23d6f3f | rernst | 02 November 2016, 09:17:03 UTC | New Mips ini file and update to sambamba v0.6.5 | 02 November 2016, 09:17:03 UTC |
| 6810df6 | rernst | 01 November 2016, 14:40:59 UTC | Use relative IAP path for strelka ini file | 01 November 2016, 14:40:59 UTC |
| af270ec | rernst | 18 October 2016, 13:10:30 UTC | Merge branch 'release-v2.4.0' into develop | 18 October 2016, 13:10:30 UTC |
| b498912 | rernst | 18 October 2016, 13:08:43 UTC | Update qdnaseq version | 18 October 2016, 13:08:43 UTC |
| 6579a90 | rernst | 18 October 2016, 08:05:34 UTC | Merge branch 'release-v2.4.0' into develop | 18 October 2016, 08:05:34 UTC |
| 3a10566 | rernst | 18 October 2016, 08:03:14 UTC | Align sambamba version with validated Dx settings | 18 October 2016, 08:03:14 UTC |
| da6e1db | rernst | 18 October 2016, 07:56:09 UTC | Merge branch 'release-v2.4.0' into develop | 18 October 2016, 07:56:09 UTC |
| 49e2243 | rernst | 18 October 2016, 07:47:52 UTC | Changed path QDNAseq to align with git tag | 18 October 2016, 07:47:52 UTC |
| d4651cd | rernst | 17 October 2016, 11:42:52 UTC | Upgrade bammetrics version | 17 October 2016, 11:42:52 UTC |
| 134fa14 | rernst | 14 October 2016, 09:25:03 UTC | Increase qdnaseq memory | 14 October 2016, 09:25:03 UTC |
| 179924d | rernst | 11 October 2016, 12:16:04 UTC | Add CHECKING_RM setting | 11 October 2016, 12:16:04 UTC |
| 6af4a8a | rernst | 11 October 2016, 10:47:46 UTC | Update bammetrics version | 11 October 2016, 10:47:46 UTC |
| c2ed0a4 | Robert Ernst | 11 October 2016, 10:37:42 UTC | Merge pull request #80 from CuppenResearch/feature-hartwig_v1.9_changes Feature hartwig v1.9 changes | 11 October 2016, 10:37:42 UTC |
| 3c92b24 | rernst | 11 October 2016, 10:33:26 UTC | Add qdnaseq support | 11 October 2016, 10:33:26 UTC |
| dd2cc16 | rernst | 11 October 2016, 10:29:54 UTC | Rename kg ini file | 11 October 2016, 10:29:54 UTC |
| d6e1581 | rernst | 28 September 2016, 08:18:09 UTC | Commit hartwig_kg_V2.2.1.ini | 28 September 2016, 08:18:09 UTC |
| 146be64 | rernst | 28 September 2016, 08:01:57 UTC | Merge branch 'release-v2.3.0' into develop | 28 September 2016, 08:01:57 UTC |
| daa8ea6 | rernst | 28 September 2016, 07:59:37 UTC | Merge branch 'master' into release-v2.3.0 | 28 September 2016, 07:59:37 UTC |
