Change Log =========== MIP v3.0 --> v4.0 mip.pl - Fixed chrY for female in SVRanking - Fixed bug in SambambaDepth causing logging to be turned off - Fixed bug causing MostCompleteBAM being incorrectly added when launching single module - Fixed bug causing info for MarkDuplicates to not be logged to qc_sampleInfo - Added flag for creating index file with GatherBAMFile. Default to TRUE - Temporary fix allowing samtools to create index for GATKBaseRecalibration BAM instead of Picard to accomodate pileup.js - Modified javaUseLargePages and reduceIO conditional statement to be implicitly boolean - Added creation of directory for analysis config file unless directory already exists - Validate all parameters - Changed percentag_mapped_reads to percentage_mapped_reads - Added Vcftools and Plink2 versions to qcmetrics - Changed default for GATKReAligner to “0” - Added SLURM QOS to sbatch header - Allowed values: [low, normal, high]. Defaults to "normal”. - Add program processing Markduplicates metric to qc_sampleInfo as “ProcessedBy” for log purpose - Remade array parameter inFilesDirs to hash parameter inFilesDir - Added CLNREVSTAT to config - Changed analysisType from scalar to hash (-at sampleID=analysisType) - Default genomes - Can be supplied from pedigree using "Sequence_type" - Enables performing analysis under correct fastq location and with correct parameters for sample specific analyses - Changed default output structure - FamilyID is now root - Data is stored under root in analysisType dir - pedigree is stored under root - scripts, mip_log, config and qc_sampleInfo are stored under FamilyID/analysis - Changed "exomes" and "genomes" to "wes" and "wgs" respectively - Added new baitset shortcut in pedigree: Agilent_SureSelectFocusedExome.V1.GRCh37_targets.bed - Modified UpdateToAbsolutePath to get info from definitions directly - Move all rio BAMProcessing to same in and out directory to enable skipping of programs - Modules that variant callers and qc modules output under their own dir, but gathered data is processed under alignment directory - Call sub in RankVariants for select file and adjust MT|M - Changed bcf generation to vcf.gz generation + tabix index - Changed rankedBCFFile to rankedBinaryFile - Changed svRankedBCFFile to svRankedBinaryFile - Changed tag in qc_SampleInfo from BCFFile to VCFBinaryFile and VCFSVBCFFile to SVBinaryFile - Change to tabix from bcf since it seems more forgiving and produce similar compression level - Added “—rank_results” in genmod score for producing rank view in Scout - Remove rank score sorting of clinical/ research - Add bwa log and HLA log to qc_sampleInfo and copying back to hds - Added decomposing using bcftools for variant callers and normalization for GATKVariantRecalibration - GRCH38 Error: Error: Field name 'phyloP46way_primate' not found dbSnpEff - phyloP46way_primate -> phyloP20way_mammalian - phyloP100way_vertebrate -> phyloP7way_vertebrate - phastCons46way_primate -> phastCons20way_mammalian - phastCons100way_vertebrate -> phastCons7way_vertebrate - Added novel calculation of F-score using plink2 - Add CLNVAR curation status (CLNREVSTAT) into rank model and bumped rank_model to version 1.17 - Added —disable_auto_index_creation_and_locking_when_reading_rods to GATKReAlign and GATKBaserecal - Added SWEREF into rank model and to default (NOTE: only car 22 pending actual release) - Added ‘variant integrity’ to sampleCheck - Modifed InbreedingFactor regExp for plink2 .het output - Added module to split fastq files, move original files to sub dir and then exit - Exchanged 'vars' for our - Made Path and outdataDirection and outDataFile be collected by recursive strategy - Let MIP detect if no affected is in pedigree and warn and turn of genmod models, score and compound - Updated VTref switch to avoid modifying same reference twice - Updated rank model to locate SIFT and PolyPhen from CSQ-field directly - Added LoFtool gene intolerance prediction to rank model - Updated rank_model to version 1.18 - Added additional sorting of SV variants after vcfanno annotation - Added extra sort of SV variants after ranking - Process SV exome|rapid as one file instead of splitted per contig to ensure that no contig will lack variants - Added insert qc metrics to qc_sampleInfo and qcmetrics - Added support for interleaved fastq files and relaxed file convention criteria - Interleaved info is gathered from fastq header for read direction 1 - BWAMem alignment is automatically adjusted accordingly - MIP now supports mixing of SE, PE and PE-interleaved files within the same fastq directory - Relaxed file convention criteria by collecting mandatory info from fastq header - just require sampleID in filename - Add fake date since this information is not recorded in fastq header for standardised file spec - Added support for metadata in yaml format (pedigree and other meta data) - MIP will look at the filending to detect file format - Set mandatory keys in Plink pedigree format to be lower case throughout in MIP output - Added additional reformating of yaml value for "sex" and "phenotype" under new keys to adhere to Plink format when required - Modified and added pedigree templates - Removed instanceTag and researchEthicalApproved - Added temp_dir to genmod annotate and filter in sub VT - Modfied pedigree file to genmod calls to use famFile and changed default to 'ped' - Modified pedigree file default ending to “.yaml” - Modified qcCollect to new yaml structure - Added sampleID level for evaluate - Cleaned up code - Added cut-offs for evaluation of mendel and father - Added collection of expected_coverage from ped.yaml and relay to qcCollect for evaluation - Removed extra feature annotations and some VEp field parsing svVcfParserRangeFeatureAnnotationColumns: - 3 = Ensembl_gene_id - REMOVED - 4 = HGNC_symbol - 5 = Phenotypic_disease_model - REMOVED - 6 = OMIM_morbid - REMOVED - 7 = Ensembl_transcript_to_refseq_transcript - REMOVED - 8 = Gene_description - REMOVED svVcfParserSelectFeatureAnnotationColumns: - 3 = HGNC_symbol - 10 = Phenotypic_disease_model - REMOVED - 11 = OMIM_morbid - REMOVED - 14 = Ensembl_gene_id - REMOVED - 16 = Reduced_penetrance - REMOVED - 17 = Clinical_db_gene_annotation - REMOVED - 18 = Disease_associated_transcript - REMOVED - 19 = Ensembl_transcript_to_refseq_transcript - REMOVED - 20 = Gene_description - REMOVED - 21 = Genetic_disease_model - REMOVED - Removed additional VEP parsing: - GeneticRegionAnnotation - HGVScp - INTRON - EXON - STRAND - HGVSc - HGVSp - Added GBCF file creation and key-path to qc_sampleInfo - Added pedigree_minimal (.fam file) and config_file_analysis to qc_sample_info - Add test of SV files in analysisrunstatus - Expect select file to have full path and not be located in MIP reference directory - Moved sacct module to case level Install.pl - Added boolean flag condaUpDate and changed flag perlInstall to boolean - Renamed preferBioConda to preferShell and made it boolean - Renamed flag update to noUpdate and made it boolean - Activated CNVnator installation - Added install script to conda env for printing software versions connected to MIP version - Added Validate parameter checks, named arguments and sub description - Updated genmod to version 3.5.6 - Added ability to set python version when creating conda env - Updated chanjo to v4.0.0 vcfParser.pl - Removed Sift and Polyhen parsing from CSQ field - Change SYMBOL to HGNC_ID in vcfparser - Added per_gene option qcCollect.pl - Changed percentag_mapped_reads to percentage_mapped_reads - Added raw total sequences and reads mapped to qcCollect - Added Vcftools and Plink2 versions to qcmetrics - Updated regExp file to version 12 MIP v2.6 --> v3.0 - Added Net/SSLeay.pm to install.pl - Added option to skip perl install - Added Manta, Delly, FT and CNVnator as structural variant callers - Added modules CombineStructuralVariants, SVVariantEffectPredictor, SVVCFParser, SVRanking - Added merging of samples in “other” chains to family chain for parallel modules - Added CNVnator version. Had to be done at start up since CNVnator does not add its version to the output. - Added Delly version on sample level - Added Manta version on sample level - Added SVVEP version and cache version - Fixed bug causing VEP version to be lost for snvs/indels - Added SVVCFParser version - Added SVGenmod/rankModel version - Added test for GATKCombineVariantsPrioritizeCaller to not include turned of variant callers - Added snpEff download of reference genome to avoid race conditions - Fixed python virtuelenvironment to not check programs if uve = 0 - Added VEP/SVVEP assembly, gencode, gene build, HGMDPublic, polyphen, regbuild, Sift, version to qcmetrics - made NIST ID settable - Removed PicardMergeSwitch, now all files are merged or renamed (single files) for more consequent naming and easier processing - Renamed ‘fileEnding’ to ‘fileTag’ and ‘removefileEnding’ to ‘fileEnding’ - Change name of BAMCalibrationAndGTBlock to only BAMCalibrationBlock - List::Util is in core module perl 5.18 replaces List::MoreUtils - Use say instead of print where relevant - Use internal Perl system commands instead of UNIX (copy, make_path) - Removed mip log file if present in config to avoid appending to old log file. Supply on log file on cmd if you want to append to log file. - Added plink2 installation via bioconda in install script - Changed binary i MIP from plink to plink2 - Added MultiQC in install script and as MIP module - Changed samtools stats module to include complete report for MultiQC processing - Made pPicardToolsMergeSamFiles mandatory: Always run even for single samples to rename them correctly for standardised downstream processing. Will also split alignment per contig and copy to temporary directory for '-rio 1' block to enable selective removal of block submodules. - Added LOFTEE VEP plugin: https://github.com/konradjk/loftee - Added LofTool VEP plugin - Added Modern::Perl ‘2014’ - Added PERL_UNICODE=SAD to install script, and hence bash_profile - stdin, stdout, and stderr to UTF‑8 as well as @ARGV and data handlers - Use UTF-8 for all source script - Added encoding UTF-8 pragma for open to default expect unicode when opening and writing - Enforce perl 5.18 version - Added autodie for generalised error and exception handling - Removed dateTime and use less cumbersome core module Time::Piece - Removed DV and added AD for samtools mpileup - Added joint calling of SV using Manta - Added SV analysis of exomes using Manta - Modified CombineSVVariants to use Delly and CNVnator on sample-level and Manta on family level - Added bcf generation of ranked vcf both select file and research - Fixed bug in temp directory - Bumped install version to 3.5.1 - Added Genmod temp dir flag - Added sacct commands to trap for each sbatch to relay progress to MIP log file.status - Made Sacct dependency into afterany - Added pPrepareForVariantAnnotationBlock - Removed pythonVirtualEnv and commands as conda is prefered - Added sourceEnvironmentCommand - Added '-pp' and '-ppm' - Add bcf conversion of select and research variants to MIP - Added check of programs mode to allowed values, more strict parsing for flaggs expecting numbers - Select variants prior to Plink processing using GATK Select variants - Move processing to node, but keept final output printing to hds - Added SV annotation using 1000G SV and vcfanno -ends - Added vcfanno, lua, config - Annotate from 1000G SV - Modified svrank_mdodel to take 1000G frequency in account - Add vcfanno version in SVCombineVariantCallSets - Updated fastqc to version 0.11.5 - Updated bwa to version 0.7.13 - Updated sambamba to version 0.6.1 - Added “—fix-mate-overlaps” to avoid counting overlapping reads twice - Removed Sambamba version from MIP flagg - Updated picardtools to version 2.3.0 - Updated Chanjo to version 3.4.1 - Updated Manta to version 0.29.6 - Updated Genmod to version 3.5.2 - Updated MultiQC to version 0.6 - Updated Vip to version 84 - Added Picardtools Markduplicates as a option and default - Added more SambambaMarkDup options - Make sambamba flagstats into subroutine to be used for all markdup - Remade capture kit options into 1 hash flag, which will build all associated files if 1 is lacking - Make Covariates to be used in the recalibration in GATKBASERCAL to be flag and array option - annotations, -Know and -knownSites - Remade VEP install assembly flag to be array and used rerun install for each assembly version - Remade SnpEff install genomeVersion flag to be array and used rerun download for each genome version - Added assembly flag to VEP script and alias it to use GRCh prefix and number - Fixed chr prefix for chanjo sex check - Updated to GATK version 3.6 - Created contig splitted target files on the fly for non genome analysis to reduce the running time of GATK Realign, BaseRecal and Haplotype - Added sub ReplaceIUPAC and used it on freebayes and samtools mpileup vcfs - Changed analysisType default from exomes to genomes MIP v2.4 --> v2.6 - Updated GATK to 3.5 - Added static binning capability for base recalibration (BQSR) - Added option --disable_indel_quals to BSQR - Added limit for exomes to only use target bases in recalibration - Added MTAF to SnpEff and vcfParser for MT frequency annotations - Added 'trio' detection to parameters instead of scriptParameters to avoid writing key to config - Fixed bug when supplying -sambambaDepthCutOffs on cmd - MIP now handles updating to absolute path for comma separated parameters correctly - Removed write to cmd string in mip log for some internal parameters - Updated install script - Added PIP to the condo env upon creation - Add check that condo is executable in system before launching rest of installation - Install script can now detect existing condo env and change cmd to accommodate - Added sambamba (0.5.9), vt (2015.11.10), bedtools (2.25.0), htslib (1.2.1) to bioconda install - Added option to prefer Bioconda install over shell for overlapping modules - Added soft link creation sub routine - Use soft link sub for sambamba (both bioconda and Shell) - Add soft link to snpEff och SnpSift for bioconda install - Update FASTQC to 11.4 via bioconda - Updated SnpEff to v4_2 via Shell - Updated Plink to v1.90b3.26 64-bit (26 Nov 2015) via shell - Updated vcfTools to 0.1.14 via SHELL - Updated Chanjo to 3.1.1 via PIP - Updated Genmod to 3.4 via PIP - Updated Picardtools to 1.141 via bioconda - Updated Samtools to 1.3 - Updated bcfTools to 1.3 - Updated htslib to 1.3 - Added picardTools installation via SHELL - Updated VEP to 83 via SHELL - Trouble with distribution - htslib and sereal (only issues with testing and not with actual running the script) - Added installation of VEP plugin UpDownDistance - Added use of VEP plugin UpDownDistance for MT contig only to avoid over annotation of the compact MT genome - Added padding to 10 nucleotides for MT in Vcfparser - Added test for undetermined in fastq file name and adjust qc-test to skip entirely for these reads - Added samtools mpileup - Added GATKCombineVariants to combine variants calls from multiple variant callers - Added generalisation for supporting multiple variant callers in MIP dependencies and GATKCombinaVariants - Added no-fail to sample check - Modified installation of picardTools and SnpEff - Add filtering to variant calls from samtools mpileup - Add samtools/bcfTools versions - Add removal of samtools pileup files - Added test::Harness for TAP summary results and future inclusion of additional test scripts - Add option to determine priority in variant callers as comma sep string - Add check of variant callers active compared to prioritise flag - Add sanity check of prioritisation flag - Add option to turn on or off installation of programs in install.pl - Added bcf file compression and indexing as sub - Added vcfTobcf sub to GATKCombineVariants - Switched vcf ready file from GATKVariantRecalibration to GATKCombineVariants - Added Freebayes variant caller - Added to removeRedundantFiles - Added Freebayes version to qcCollect - RemoveRedundant files info is now recorded in definition.yaml - Added GATKCombineVariants to removeRedundant files - Add bcftools norm to samtools pileup and freebayes output - Add lastlogFilePath to qc_sampleInfo - Made lanes and readDirections info more nested - Add 1000G Phase 3 and Exac to Genmod annotation - Changed regEx in test.t to include all until “,” for INFO fields in Header - Modified bioconda softlinks sub call to only execute if programs are installed - Added MT.codon table sub for snpEff config to install script - Remake GENMOD CADD file option to array - Added padded target intervals to exome analysis again for GATKRealign and GATKHaplotypeCaller - Reactivate GATKPaddedTarget parameter - Made associatedPrograms arg into an array instead of a comma sep string - Fixed check for when a capture kits is lacking from input and fallback to using “latest” - Remade CheckParameterFiles to work with DataType - Add evaluation with NIST as a module in MIP - Fix the . mip.sh to bash mip.sh - Added reference to define/definitions - CheckParameterFiles now works with parameterExistsCheck directly instead of “d” and “f” enabling merge of directory and file sections - Changed if for intervalListFile to be if($IntervalList ) instead of analysisTypeExome|rapid - Add programType=Aligner to define/definitions - Remade sanity check of aligner to count if more than 1 aligner has been switched on (MosaikAligner, BWASampe, BWAMEM) - Dynamic setting of ‘aligner’ depending in aligner supplied by outDirectoryName - Renamed aligner to alignerOutDir - Added genmod max_af - Added canonical to VEP features MIP v2.0 --> v2.4 - Bugfixes - Updated most program version (see docs) and databases - Logs versions and databases - Added -pVT - Added -allSites option to GenoTypeVCFs - Added version tag to definitions.yaml - Cleaned some old parameter names - Added test for parameter compatibility between defineParameters.yaml and config - Added new parameter snpSiftAnnotationOutInfoKey - Changed SnpSift_ for 1000G and EXACAF to facilitate downstream processing since both work on KEY=AF - Remade dbsnpAF parsing to accommodate multiple entries for the same env - Added vt decompose and normalise subroutine for both reference and variant vcf - Removed vcf_parser —split - MIP now works only on config tags from select file meta data header for select genes - Added genmod version and removed RankVariants version - Add test for VEP cache and directory version linked - Added option OverclippedReadFilter to GATKBaseRecalibration/PrintReads - Exchange grep for any in array check and use eq instead of // for stringency - Added vt decompose and normalise subroutine call for relevant downloadable references ("indels", "mills", "dbsnp", "hapmap", "dbsnpex", "1000g_snps") - Add check for ingoing references that VT has been used if VT is on - Fixed bug in AnalysisRunStatus modules caused when first processing -rio 1 and then -rio 0 - Fixed bug when adding samples to pedigree to already processed samples - Removed Radial:sw and LR_score from dbNSFP annotation as these have become obsolete - Remade RemoveRedundant files - Added bcf compression alternativ - Added perl oneliner to VT that removes '*' alt.allele after decomposing as it does not add any new info MIP v1.0 --> v2.0 - Major code refactoring - Bugfixes - Updated most program version (see docs) and databases - Logs versions and databases - Removed modules -pMerge_anvar, -pAdd_dp - MIP no longer creates master templates, instead this is taken care of dynamically - Added -pVeP, -pSnE, -pVcP -pChanjoSexCheck - Module PicardSortSam is now integrated in alignment modules - Use VCF format where appropriate - Created standardised VCF list levels (",", ":", "|") - Clinical transcripts are selected after VEP annotation using VCFParser - Removes ethical issue with overlapping genes - Full resolution in annotation - Gene - Transcripts - Multiple alleles - Split multi allelic calls into single records - Use SO terms - Calculate Sift an PolyPhen per transcript and allele - Remade transcript and cDNA and protein info from VEP CSQ field - Switched from MAF to AF - Use Log4Perl for logging - All processes create temp directory on (default @nodes) - Creates automatic migration to and from nodes - Deploy more aggressive scatter/gather technique. Processing per contig whenever possible. - Analyse order in contig size not number - Use piping in SnpSift annotation and where possible - Reduce IO between nodes using -rio flag. Will run modules sequentially where appropriate. - Created automatic removal of files when appropiate at tempDir * Flag changes - -huref/--humanGenomeReference --> -hgr/--humanGenomeReference - -rea/--researchEthicalApproval Tag for displaying research candidates in Scout (defaults to "notApproved") - -tmd/--tempDirectory Set the temporary directory for all programs (defaults to "/scratch/SLURM_JOB_ID";supply whole path) - -nrm/--nodeRamMemory The RAM memory size of the node(s) in GigaBytes (Defaults to 24) - -ges/--genomicSet Selection of relevant regions post alignment (Format=sorted BED; defaults to "") - -rio/--reduceIO Run consecutive models at nodes (defaults to "0") - -l/--logFile Mip log file (defaults to "{outDataDir}/{familyID}/mip_log/{timestamp}/{scriptname}_{timestamp}.log") - -pGZ/--pGZip --> -pGZ/--pGZipFastq - -pFQC/--pFastQC --> -pFqC/--pFastQC - -moaannpe/--mosaikAlignNeuralNetworkPeFile --> -moaape/--mosaikAlignNeuralNetworkPeFile - -moaannse/--mosaikAlignNeuralNetworkSeFile --> -moaase/--mosaikAlignNeuralNetworkSeFile - -pBWA_mem/--pBwaMem --> -pMem/--pBwaMem - -bwamemrdb/--bwaMemRapidDb --> -memrdb/--bwaMemRapidDb - -pBWA_aln/--pBwaAln --> -pAln/--pBwaAln - -pBWA_sampe/--pBwaSamp --> -pSap/--pBwaSampe - -picardpath/--picardToolsPath --> -ptp/--picardToolsPath - -picttmpd/--PicardToolsTempDirectory --> removed - -pPicT_sort/--pPicardToolsSortSam --> removed - -pPicT_merge/--pPicardToolsMergeSamFiles --> -pPtM/--pPicardToolsMergeSamFiles - -pPicT_mergerr/--pPicardToolsMergeRapidReads -> -pPtMR/--pPicardToolsMergeRapidReads - -picT_mergeprev/--picardToolsMergeSamFilesPrevious --> -ptmp/--picardToolsMergeSamFilesPrevious - -pPicT_markdup/--pPicardToolsMarkduplicates --> -pPtMD/--pPicardToolsMarkduplicatesWithMateCigar - -pCh_B/--pChanjoBuild --> -pChB/--pChanjoBuild - -pChS/--pChanjoSexCheck - -pCh_C/--pChanjoCalculate --> -pChA/--pChanjoAnnotate - -chccut/--chanjoCalculateCutoff --> -chacut/--chanjoAnnotateCutoff - -pCh_I/--pChanjoImport --> -pChI/--pChanjoImport - -pCC_bedgc/--pGenomeCoverageBED --> -pGcB/--pGenomeCoverageBED - -xcov/--xCoverage --> -gcbcov/--GenomeCoverageBEDMaxCoverage - -pCC_picmm/--pPicardToolsCollectMultipleMetrics --> -pPtCMM/--pPicardToolsCollectMultipleMetrics - -pCCE_pichs/--pPicardToolsCalculateHSMetrics --> -pPtCHS/--pPicardToolsCalculateHSMetrics - -extbl/--exomeTargetBedInfileLists --> -ptchsetl/--exomeTargetBedInfileLists - -extpbl/--exomeTargetPaddedBedInfileLists --> -ptchsetpl/--exomeTargetPaddedBedInfileLists - -pRCP/--pRCovPlots --> -pRcP/--pRCovPlots - -gatkpath/--genomeAnalysisToolKitPath --> -gtp/--genomeAnalysisToolKitPath - -gatkbdv/--GATKBundleDownLoadVersion --> -gbdv/--GATKBundleDownLoadVersion - -gatktmpd/--GATKTempDirectory --> removed - -gatktpbl/--GATKTargetPaddedBedIntervalLists --> -gtpl/--GATKTargetPaddedBedIntervalLists - -gatkdcov/--GATKDownSampleToCoverage --> -gdco/--GATKDownSampleToCoverage - -pGATK_real/--pGATKRealigner --> -pGrA/--pGATKRealigner - -gatkrealknset1/--GATKReAlignerINDELKnownSet1 --> -graks1/--GATKReAlignerINDELKnownSet1 - -gatkrealknset2/--GATKReAlignerINDELKnownSet2 --> -graks2/--GATKReAlignerINDELKnownSet2 - -pGATK_baserecal/--pGATKBaseRecalibration --> -pGbR/--pGATKBaseRecalibration - -gatkbaserecalknset/--GATKBaseReCalibrationSNPKnownSet --> -gbrkse/--GATKBaseReCalibrationSNPKnownSet - -pGATK_hapcall/--pGATKHaploTypeCaller --> -pGhC/--pGATKHaploTypeCaller - -gatkhapcallsnpknset/--GATKHaploTypeCallerSNPKnownSet --> -ghckse/--GATKHaploTypeCallerSNPKnownSet - -pGATK_genotype/--pGATKGenoTypeGVCFs --> -pGgT/--pGATKGenoTypeGVCFs - -gatkgenotyperefgvcfinfile/--GATKGenoTypeGVCFsRefGVCFInfile --> -ggtgrl/--GATKGenoTypeGVCFsRefGVCF - -pGATK_varrecal/--pGATKVariantRecalibration --> -pGvR/--pGATKVariantRecalibration - -gatkexrefsnp/--GATKExomeReferenceSNPs --> -gvrtss/--GATKVariantReCalibrationTrainingSetDbSNP - -gatkvarrecaltrhapmap/--GATKVariantReCalibrationTrainingSetHapMap --> -gvrtsh/--GATKVariantReCalibrationTrainingSetHapMap - -gatkvarrecaltrd1000Gsnp/--GATKVariantReCalibrationTrainingSet1000GSNP --> -gvrtsg/--GATKVariantReCalibrationTrainingSet1000GSNP - -gatkvarrecaltromni/--GATKVariantReCalibrationTrainingSet1000GOmni --> -gvrtso/--GATKVariantReCalibrationTrainingSet1000GOmni - -gatkvarrecaltrdbmills/--GATKVariantReCalibrationTrainingSetMills --> -gvrtsm/--GATKVariantReCalibrationTrainingSetMills - -gatkvarrecaltsfilterlevel/--GATKVariantReCalibrationTSFilterLevel --> -gvrtsf/--GATKVariantReCalibrationTSFilterLevel - -gvrevf/--GATKVariantReCalibrationexcludeNonVariantsFile - -gvrsmr/--GATKVariantReCalibrationSpliMultiRecord - -pGATK_phaseTr/--pGATKPhaseByTransmission --> -pGpT/--pGATKPhaseByTransmission - -pGATK_readPh/--pGATKReadBackedPhasing --> -pGrP/--pGATKReadBackedPhasing - -gatkreadphphaseqthr/--GATKReadBackedPhasingPhaseQualityThresh --> -grpqth/--GATKReadBackedPhasingPhaseQualityThreshold - -pGATK_varevalall/--pGATKVariantEvalAll --> -pGvEA/--pGATKVariantEvalAll - -pGATK_varevalexome/--pGATKVariantEvalExome --> -pGvEE/--pGATKVariantEvalExome - -gatkvarevaldbsnp/--GATKVariantEvalDbSNP --> -gveedbs/--GATKVariantEvalDbSNP - -gatkvarevaldbgold/--GATKVariantEvalGold --> -gveedbg/--GATKVariantEvalGold - -pANVAR/--pAnnovar --> -pAnV/--pAnnovar - -anvarpath/--annovarPath --> -anvp/--annovarPath - -anvargbv/--annovarGenomeBuildVersion --> -anvgbv/--annovarGenomeBuildVersion - -anvartn/--annovarTableNames --> -anvtn/--annovarTableNames - -anvarstn/--annovarSupportedTableNames --> -anvstn/--annovarSupportedTableNames - -anvarmafth/--annovarMAFThreshold --> -anvarmafth/--annovarMAFThreshold - -pVeP/--pVariantEffectPredictor Annotate variants using VEP (defaults to "1" (=yes)) - -vepp/--vepDirectoryPath Path to VEP script directory (defaults to ""; supply whole path) - -vepc/vepDirectoryCache Specify the cache directory to use (supply whole path, defaults to "") - -vepf/--vepFeatures VEP features (defaults to ("refseq","hgvs","symbol","numbers","sift","polyphen","humdiv"); comma sep) - -pVcP/--pVCFParser Parse variants using vcfParser.pl (defaults to "1" (=yes)) - -vcpvt/--vcfParserVepTranscripts Parse VEP transcript specific entries (defaults to "0" (=no)) - -vcprff/--vcfParserRangeFeatureFile Range annotations file (defaults to ""; tab-sep) - -vcprfa/--vcfParserRangeFeatureAnnotationColumns Range annotations feature columns (defaults to ""; comma sep) - -vcpsf/--vcfParserSelectFile File containging list of genes to analyse seperately (defaults to "";tab-sep file and HGNC Symbol required) - -vcpsfm/--vcfParserSelectFileMatchingColumn Position of HGNC Symbol column in SelectFile (defaults to "") - -vcpsfa/--vcfParserSelectFeatureAnnotationColumns Feature columns to use in annotation (defaults to ""; comma sep) - -pSnE/--pSnpEff Variant annotation using snpEFF (defaults to "1" (=yes)) - -snep/--snpEffPath Path to snpEff. Mandatory for use of snpEff (defaults to "") - -snesaf/--snpSiftAnnotationFiles Annotation files to use with snpSift (comma sep) - -snesdbnsfp/--snpSiftDbNSFPFile DbNSFP File (defaults to "dbNSFP2.6.txt.gz") - -snesdbnsfpa/--snpSiftDbNSFPAnnotations DbNSFP annotations to use with snpSift (defaults to ("SIFT_pred","Polyphen2_HDIV_pred","Polyphen2_HVAR_pred","LRT_pred","MutationTaster_pred","GERP++_NR","GERP++_RS","phastCons100way_vertebrate","1000Gp1_AF","ESP6500_AA_AF"); comma sep) - -pRankVar/--pRankVariants --> -pRaV/--pRankVariants - -rs/--rankScore --> removed - -gf/--geneFile --> -ravgf/--geneFile - -imdbfile/--ImportantDbFile Important Db file (Defaults to "") --> removed - -imdbte/--ImportantDbTemplate Important Db template file used to create the specific family '-im_dbmf' master file (Defaults to "") --> removed - -imdbmf/--ImportantDbMasterFile Important Db master file to be used when selecting variants (defaults to "{outDataDir}/{familyID}/{familyID}.intersectCollect_selectVariants_db_master.txt";Supply whole path) --> removed - -imdbfof/--ImportantDbFileOutFiles The file(s) to write to when selecting variants with intersectCollect.pl. Comma sep (defaults to "{outDataDir}/{familyID}/{aligner}/GATK/candidates/ranking/{familyID}_orphan.selectVariants, {outDataDir}/{familyID}/{aligner}/GATK/candidates/ranking/clinical/{familyID}.selectVariants"; Supply whole path/file) --> removed - -ravcs/--caddWGSSNVs Annotate whole genome sequencing CADD score (defaults to "0" (=no)) - -ravcsf/--caddWGSSNVsFile Whole genome sequencing CADD score file (defaults to "whole_genome_SNVs.tsv.gz") - -ravc1kg/--cadd1000Genomes 1000 Genome cadd score file (defaults to "0" (=no)) - -ravc1kgf/--cadd1000GenomesFile 1000 Genome cadd score file (defaults to "1000G.tsv.gz") - -ravwg/--wholeGene Allow compound pairs in intronic regions (defaults to "1" (=yes)) - -ravrm/--rankModelFile Rank model config file (defaults to "") - -pSCheck/--pSampleCheck --> -pScK/--pSampleCheck - -pQCC/--pQCCollect --> -pQcC/--pQCCollect - -QCCsampleinfo/--QCCollectSampleInfoFile --> -qccsi/--QCCollectSampleInfoFile - -QCCregexp/--QCCollectRegExpFile --> -qccref/--QCCollectRegExpFile - -pREM/--pRemovalRedundantFiles --> -pReM/--pRemoveRedundantFiles - -pAR/--pAnalysisRunStatus --> -pArS/--pAnalysisRunStatus