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