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