| refs/tags/v2.3.0 | v2.3.0 | 7b039bd | New features: Sex aware variant calling + new haplotypecaller scala script -> add CALLING_SEXAWARE to ini Using relative paths for qscripts and IAP scripts Save submission log automatically Add flagstat stats to bamMetrics -> needs new version of bamMetrics Bug fixes: Delly job submission Delly chromosome chunks | 28 September 2016, 08:00:54 UTC |
| refs/tags/v2.2.1 | v2.2.1 | 6aaf4bf | - Somatic melt script v2. - Add sambamba parameter to ExonCov command, solves #75. - Add BAF settings to ini files. - Better plotting for BAF analysis. | 17 June 2016, 12:07:38 UTC |
| refs/tags/v2.2.0 | v2.2.0 | 6b00b82 | - Callable loci module - Move realign bam after flagstat check, solves #70 - Somatic melt script: Check input tumor sample name with name in vcf - Fix pileup error message - Improve prestats checking, partly solves #67 - Remove pileup if IAP done, solves #12 and #72 - Add manta - Replace SOMVAR_REGEX and CNV_REGEX by SOMATIC_REGEX setting, also used in new manta sv analysis. - Add 'tmp' steps to mapping module, move to definitive files if flagstats check succeeds | 01 June 2016, 08:33:28 UTC |
| refs/tags/v2.1.0 | v2.1.0 | a80e242 | - BAF Analysis. - Chunk mutect per chr. - Replace bio-vcf filter by snpsift filter for freebayes. - Changes to ini and iap to analyse wgs data on the new UMC hpc setup. | 18 March 2016, 10:25:06 UTC |
| refs/tags/v2.0.0 | v2.0.0 | 831bf1a | IAP v2.0.0 release, only compatible with CentOS7 cluster setup. - New sge module, containing qsub templates which use the new time and mem variables. - New karyotypeplot. - Seperate markdup settings from mapping settings. - Send done email after tmp files are removed. - Added bam.bai fro realigned and recalibrated bams. - Added option to change filtered variant types. - Moved old centos6 ini's to seperate folder. | 01 March 2016, 07:55:45 UTC |
| refs/tags/v1.4.0 | v1.4.0 | 13aa6c3 | - Overflow-list-size option, used in sambamba dedup. #32 - Chunk varscan and freebayes per chr. - Add mapping settings to ini (-c and -M). #43 - File checking improvements, use -s instead of -f to check whether file is not empty as well. - Upgrade picard to 1.141 for all ini files. Bugfixes: - Make somatic_targets optional. - Only merge mutect passed variants. #45 - Fix .bam replacement regex at multiple locations. #40 - Use correct threads settings for pileup. - Add separate path for king, solves. #42 | 18 January 2016, 11:51:33 UTC |
| refs/tags/v1.3.0 | v1.3.0 | 8d0c7e3 | - DX NIPT - DX exome and panel options - SV calling using delly - Paralel pileup - Memory specification changed, remove multiplication by threads. | 10 December 2015, 10:23:14 UTC |
| refs/tags/v1.2.9 | v1.2.9 | 067cebb | - Hotfix: Fix .bam removal if realignment is finished | 16 September 2015, 11:47:00 UTC |
| refs/tags/v1.2.8 | v1.2.8 | a095f32 | - Update to sambamba v0.5.8 - Cleanup module and function descriptions - Remove unused illumina metrics scripts - Add somatic variants and copy number sample regex to ini files | 19 August 2015, 14:48:27 UTC |
| refs/tags/v1.2.7 | v1.2.7 | d9bfe92 | - Add dbsnp id to merged somatic vcf - Update SnpEff to v4.1_H | 05 August 2015, 09:26:02 UTC |
| refs/tags/v1.2.6 | v1.2.6 | 5b5803d | - Enable -debug for bammetrics - Add --tmp-dir to sample markdup step. | 23 July 2015, 07:20:44 UTC |
| refs/tags/v1.2.5 | v1.2.5 | 323be2b | - Add FREEC to copynumber tools, solves #17. - New vcfutils module, containing: kinship anlysis and phase by transmision, solves #3 and #4. - Replace plotilluminametrics with bamMetrics tool. - Add sample markdup option, solves #2. - Add dbsnp parameter to genotypeGVCF, solves #18. - Add -P to all qsub commands and replace module project variables by cluster_project variable. - Update to picard v135. - Update to gatk v3.4-46. - Update to sambamba v0.5.6. - Use Sambamba to create pileups, solves #13. | 20 July 2015, 11:54:07 UTC |
| refs/tags/v1.2.4 | v1.2.4 | 8231e0c | - Hotfix: Add set names to somatic vcf merge command | 12 June 2015, 14:11:59 UTC |
| refs/tags/v1.2.3 | v1.2.3 | 4368f32 | - Qscript to genotype multiple g.vcf files - Contra plot script to contra analysis, solves #8 - Basic annotation to merged somatic variants file, solves #7 - Support for starting IAP with BAM and FASTQ files, solves #15 - Update Cosmic database to v72 - Fix path to strelka ini files | 02 June 2015, 14:09:35 UTC |
| refs/tags/v1.2.2 | v1.2.2 | e48195c | - Add tmpdir option to sambamba jobs - Add seperate jobs and settings for flagstat - Improved error messages - Added check and continue control for each mapping step - Update FastQC to v0.11.3 - Update snpEff to v4.1e - Update CPCT somatic variant sample name regex | 08 May 2015, 08:48:08 UTC |
| refs/tags/v1.2.11 | v1.2.11 | 1f11919 | - Fix issue with fastq and bam find when creating a config file. | 02 November 2015, 12:41:27 UTC |
| refs/tags/v1.2.10 | v1.2.10 | c27e960 | - Add mutect to somatic variant analysis (for now without queue). - Add gemMappability to freec config, #19. - Intermediate strelka results will now be removed when strelka is done. - Check last line of vcf after annotation step, #20. - Create md5sum of the output directory if iap finished successfully, # 16. - Fix memory allocation for annotate jobs (mem * threads), #21. | 22 October 2015, 08:32:41 UTC |
| refs/tags/v1.2.1 | v1.2.1 | 29807d0 | - When starting with bam input, check and/or symlink flagstat and bai. - Add scatter and nct to genotypeGVCF - Set queue calling job memory - Seperate log file for each poststats job - Bugfix: Change working bam before skipping a bqsr job if .done file present - Bugfix: Added check for ref samples when running illumina_check for somatic jobs - Seperate jobs for BQSR flagstats | 10 April 2015, 10:12:20 UTC |
| refs/tags/v1.2.0 | v1.2.0 | c555ef0 | - Add copy number support using contra. - Check config files before submitting jobs. | 12 March 2015, 11:58:23 UTC |
| refs/tags/v1.1.2 | v1.1.2 | 5ed5e8e | - Somatic variants extra checks and enhancements. - Update to snpeff v4.1b - Update to dbnsfp 2.9 | 03 March 2015, 09:05:58 UTC |
| refs/tags/v1.1.1 | v1.1.1 | 8edf43f | - Hotfix: Merge somatics, add GT to Strelka calls. - Update to dbNSFP v2.8 | 03 February 2015, 09:29:56 UTC |
| refs/tags/v1.1 | v1.1 | ac4301f | Add somatic variant callers to IAP. | 23 January 2015, 12:54:36 UTC |
| refs/tags/v1.0.9 | v1.0.9 | b753705 | Increased --overflow-list-size and mapping .done regex bugfix | 06 November 2014, 10:24:04 UTC |
| refs/tags/v1.0.8 | v1.0.8 | 96a66b4 | Update to dbNSFPv2.7 | 31 October 2014, 11:18:38 UTC |
| refs/tags/v1.0.7 | v1.0.7 | 35e43b6 | Mark duplicates is now optional and must be set in the .ini files | 03 October 2014, 12:57:07 UTC |
| refs/tags/v1.0.6 | v1.0.6 | 17d89fb | Features: - BAM and VCF input support - WGSMetrics - gatk -retry function for Qscripts - PU in readgroup - Removed samtools dependency | 22 September 2014, 12:52:18 UTC |
| refs/tags/v1.0.5 | v1.0.5 | 88cd1d5 | Bugfix in plotIlluminaMetrics for runs with 9 or more samples. | 06 June 2014, 06:42:21 UTC |
| refs/tags/v1.0.4 | v1.0.4 | c6405ee | Added Miseq support and random colors for plots with 9 or more samples. | 03 June 2014, 10:58:33 UTC |
| refs/tags/v1.0.3 | v1.0.3 | f907f52 | Fix for a lot of samples and numeric sample names | 28 May 2014, 12:58:11 UTC |
| refs/tags/v1.0.2 | v1.0.2 | 2d0f649 | Support for parent dirs and short opts in createConfig. | 27 May 2014, 12:36:36 UTC |
| refs/tags/v1.0.11 | v1.0.11 | 2ab82b6 | Bugfix HardFilter.scala Added SnpSift GoNL annotation | 15 January 2015, 12:28:45 UTC |
| refs/tags/v1.0.10 | v1.0.10 | e097481 | - Support for non diploid organisms - SnpEff v4 update - Added -no-downstream -no-upstream -no-intergenic flags to SnpEff command | 03 December 2014, 09:26:03 UTC |
| refs/tags/v1.0.1 | v1.0.1 | cedfff6 | Features: Print version tag and copy used .ini file to log directory. UMCU exome settings: Added new calling target.list with 20bp padding. | 13 May 2014, 09:30:04 UTC |
| refs/tags/v1.0 | v1.0 | bad1349 | Version to 1.0 | 07 May 2014, 10:55:09 UTC |
