Original Author: Kortine Kleinheinz [email protected]
Current Author: Gregor Warsow [email protected]
ACEseq (Allele-specific copy number estimation with whole genome sequencing) is a tool to estimate allele-specific copy numbers from human WGS data, and comes along with a variety of features:
- GC/replication timing Bias correction
- quality check
- SV breakpoint inclusion
- automated estimation of ploidy and tumor cell content
- HRD/TAI/LST score estimation
- with/without matched control processing
Kortine Kleinheinz, Isabell Bludau, Daniel Huebschmann, Michael Heinold, Philip Kensche, Zuguang Gu, Cristina Lopez, Michael Hummel, Wolfram Klapper, Peter Moeller, Inga Vater, Rabea Wagener, ICGC MMML-Seq project, Benedikt Brors, Reiner Siebert, Roland Eils, Matthias Schlesner. ACEseq - allele specific copy number estimation from whole genome sequencing. biorxiv.
The complete installation instructions can be found in the documentation.
Additional necessary software like e.g. Roddy can be found here
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Version update 6.0.0
- Changed the phasing routine. The program "impute2" was replaced by "Beagle". Files and tools were renamed accordingly.
- Generally renamed all tools and files from "imputeGenotype" to "phaseGenotype" (and so on) as the subroutine does not actually perform imputation but rather phasing.
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Version update to 5.0.1
- fixed density(NA) bug and index bug for frequencies (as.character) in clustering step
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Version update to 5.0.0
- introduced CNA.type 'AMP' (TCN>=2*ploidy + 1)
- do not use ChrX/Y for round/full ploidy determination
- fixed faulty assignment of 'neutral' to gonosomal segments in male samples
- fixed pruning bug (combineNeighbours, homozygousDel)
- force gender to be set in noControl cases
- enhanced cluster plots
- added CovBaf plots
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Version update to 4.0.3
- use fake controls from shared folder
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Version update to 4.0.2
- fixed several gap merging bugs (HRD score)
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Version update to 4.0.1
- smoothing: merge first segment after long gap
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Version update to 4.0.0
- fixed bug in HRD score determination (tcnStatePerChrom nrow vs length)
- write out file with segments contributing to HRD score
- introduced HRD score with gapped centromeres (numberHRDSmoothReduced)
- corrected LST and TAI calculation (changed centromere regions file)
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Version update to 3.0.0
- fixed 'artifact-1' artifact (allow for low purity solutions in this case)
- work with old (version < 2.x) ACEseq result files on rerun
- introduced ymaxcov_threshold for maximum TCN count represented in segment plots
- fixed bug in creation of json file (doubled first solution)
- fixed noControl filegroup bug
- fixed noControl control-bam file access issue
- run without SV in noControl cases
- use true|false for SV cvalue and not yes|no
- fixed bug contamination/sample swap detection (secondPeak index)
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Version update to 2.0.0
- add contours in 2D plots
- add 1.0 (instead of 0.00001) to lengths when getting log2 for weights to consider segments with length=1
- Add flags and checks for handling the sv file and remove null pointer exceptions
- fix bug in tcc ploidy estimation
- parametrized local minimum upper boundary (local_minium_upper_boundary_shift)
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Version update to 1.2.10
- add bioconda dependencies
- replace all occurences of qq.R and getopt2 by getopt
- replace all occurenced of name delly and crest, also in final output
- change color for deletions(red ==>blue) and duplications (red ==> blue)
- enable modularization of workflow
- remove generateVCF job, add estiate HRD score
- remove dependency of haploblock files in cluster_and_prune_segments
- add HRD score estimation, smooth segments and filter for blacklist segments
- add 0.00001 to lengths when getting log2 for weights to consider segments with length=1, which will be merged in a future release
- adjust colors for clustering so they are consistent across all three cluster plots
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Version update to 1.2.8-1
- remove vcf creation in final job (obsolete)
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Version update to 1.2.8
- comb_pro_extra and most_important_info contain X and Y
- removed GNL column
- new annotation of CNA.type (DEL/DUP/LOH/TCNNeutral/NA)
- new estimation of quality (length of subclonal over total mapped)
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Version update to 1.2.7-1/2
- removed dependencies on coConfigurations
- change of svOutputdirectory and set to default SOPHIA
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Version update to 1.2.7
- addition of tumorSample and controlSample variable as read out from bam file
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Version update to 1.2.6-*
- bugfix allowing coordinates for chrom2 in SV file to be smaller than chrom1 coordinates
- bugfix allowing chrom1 being decoy chromosome in case chrom2 is autosome|X|Y
- bugfix plots using print and ggplot2:ggsave to generate plots
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Version update to 1.2.6
- runparallel for impute moved from COWorkflows to ACEseqMethods.groovy
- sort most_important_info and comb_pro_extra file
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Version update to 1.2.1
- enable BAF plots as extra step, that is only run for paired workflow and only writes down checkpoint
- enable json with quality parameters for closest to diploid solution, should be read out by otp, file noted down in config.xml
- enable upgrade to R-3.3.1, R-2.15.0 is only working with exception (pscbs_all_R_2.15.R must be redefined as tool and path to pscbs lib should be given)
- better format of cnv_parameter files
- removed "set -x", pipefail etc.
- PSCBSgabs_delly.py
- improved code
- added selective column
- add noControl options
- cluster and prune take mean if two equally high peaks appear or for single peak remove bug
- add chromosome labels to general coverage plots
- remove chr prefixes throughout analysis
- make email option optional for gcCorrection
- be flexible on sv_type file, "id" column optional
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Version update to 1.0.189
- pscbs_all.R: bugfix that screwed up chrlength
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Version update to 1.0.187
- stabilizing addition to pscbs_all.R
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Version update to 1.0.185
- bugfixes for pscbs_all.R
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Version update to 1.0.183
- pscbs_all.R and PSCBSall.sh:
- scientific format of start and end here already, replace +Inf/-Inf with chromosome length/0
- adjustsAlleleFreqs and functions.R and purity_ploidy.R:
- don't consider dbSNP position with 0 reads mapped in tumor
- manual_pruning.R:
- don't consider dbSNP position with 0 reads mapped in tumor and remove bug in case no main cluster is found
- pscbs_all.R and PSCBSall.sh:
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Version update to 1.0.181
- convertTabTovcf.sh: moved usage of id option (for pcawg output)
- convertToVcf.py:
- libraries removed
- default for id argument set (NA)
- changed version number (for pcawg output)
- added missing "\n" for header
- added SAMPLE_ID line for header (pancan)
- changed sample_$pid column name to TUMOR
- correctGCBias_functions.R:
- corrected coordinates in coverage plots
- datatablePSCBSgaps.sh:
- tabix for position not window (col5 instead of 1)
- haplotypes.sh:
- tabix corrected (added -e)
- manual_pruning.R:
- adjusted for no cluster within cluster limits
- merge_and_filter_cnv.py/merge_and_filter_snp.py:
- removed coverage filter for tumor
- pscbs_all.R:
- round coordinates with .5 (ceiling for start, floor for end)
- PSCBSgabs_plus_delly_points.py:
- removed library
- pscbs_plots_functions.R:
- fullPloidy calculation by largest fraction of genome instead of most segments in genome
- annotation of LOH (cn,gain,loss) corrected
- LOH definition adjusted instead of dhMean </> 0.8 using round(c1) and round(c2) (==0 for LOHs, != 0 for everything else)
- pscbs_plots.R:
- added gc()
- purity_ploidy.R:
- average coverage on autosomes instead of all chromosomes (better for males)
- allow missing autosomes
- vcfAnno.sh:
- rearranged order of script (first gender estimation)
- addition of fake control option:
- added scripts:
- replaceControl.sh
- replaceControlACEseq.R
- added scripts:
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Version update to 1.0.158
- extracted into single plugin
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Version update to 1.0.131
- plots: tab seperateed file with cnv parameters written
- correctGCBias: extra file with qc parameters printed, conversion to json, parameter for scale adjustion added
- Change workflow class to override another execute method. This makes the workflow a bit cleaner.
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Version update to 1.0.114
- PSCBSgabs_plus_CRESTpoints.py: add identifier column to sv_points file (used with DELLY calls)
- PSCBSgabs_plus_delly_points.py: add identifier column to sv_points file, convert start coordinates to 1-based
- homozygous_deletion.pl: added id column for sv file, adjust length calculation to inclusion of start AND End coordinate
- correctGCBias.R: density estimation without restrictions for final corrected covRatio
- manual_pruning.R: check for haploblock files to prevent script from failing after 2 hours due to missing files, plot Names with PID, new feature: merge clusters again after outlier removal and choose random cluster if 2 or more "mainClusters are found"
- purity_ploidy.R: estimate and report average coverage, add minCoverage as optional parameter
- purity_ploidy_estimation_final.R: bug fixes for balanced segments using wrong matrix, new feature: disallow copy number states of 0, don't punish balanced segments with copy number down to -0.3
- functions.R: soft limits for control SNPs used for peak calling (coverage dependant), no limits for tumor SNPs, single threat for running
- purityPloidity_EstimateFinal.sh: add PID as parameter
- analysisCopyNumberEstimation.xml: adjust settings for peak calling to actually used resources
- pscbs_plots_functions.R: convert 0.5 coordinates to integer values, don't allow scientific format for output files
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Version update to 1.0.109
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Version update to 1.0.105
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Version update to 1.0.104
- bug fix: read all lines of breakpoint.txt to avoid missing information on chr 1
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Version update to 1.0.103