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GotCloud: Variant Calling Options (view source)

Revision as of 14:28, 24 October 2014

6,752 bytes added ,  14:28, 24 October 2014
→‎Miscellaneous Options
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| --nophonehome ||  || disable phonehome in GotCloud and the tools it calls ||  
 
| --nophonehome ||  || disable phonehome in GotCloud and the tools it calls ||  
 
|-
 
|-
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| || BAMUTIL_THINNING || thinning parameter for bamUtil programs (will be set to 0 - if --nophonehome is specified) || --phoneHomeThinning 10
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|-
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|}
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==== Directory Settings Options ====
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These values set GotCloud output subdirectories (relative paths under the OUT_DIR directory).  You should not need to change these from the defaults unless you want to use different sub-directory names.
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Configuration Key !! Value Description !! Default Value
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|-
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| BAM_GLF_DIR || GLF outputs per BAM (if multiple BAMs per sample) (intermediate files) || glfs/bams
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|-
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| SM_GLF_DIR || GLF outputs per sample (intermediate files) || glfs/samples
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|-
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| '''VCF_DIR''' || unfiltered and filtered VCFs || vcfs
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|-
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| PVCF_DIR || vcfPileup results (intermediate files) || pvcfs
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|-
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| SPLIT_DIR || VCFs with PASS variants only & split into multiple files || split
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|-
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| BEAGLE_DIR || beagle output || beagle
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|-
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| SPLIT4_DIR || VCFs with PASS variants only & split into multiple files for running beagle4 || split4
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|-
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| BEAGLE4_DIR || beagle version 4 output || beagle4
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|-
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| THUNDER_DIR || thunder output || thunder
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|-
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| TARGET_DIR || directory to store target information when running with a BED file || target
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|-
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| GLF_INDEX || filename for index file needed for glfflex (file is created by GotCloud) || glfIndex.ped
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|-
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|}
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==== Tool Options ====
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These values set the binaries GotCloud should use.  You should not need to change these from the defaults unless you want to try a different version of one of the tools.
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Some tools have the options specified with the binary command, while others have them separate or hard coded
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Configuration Key !! Program Description !! Default Value
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|-
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| SAMTOOLS_FOR_PILEUP || samtools to use for pileup || $(BIN_DIR)/samtools-hybrid
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|-
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| SAMTOOLS_FOR_OTHERS || samtools to use for view and calmd || $(BIN_DIR)/samtools-hybrid
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|-
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| GLFMERGE || merge glf files when there are multiple BAMs per indvidual || $(BIN_DIR)/glfMerge
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|-
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| GLFFLEX || perform glf-based variant calling (replacement for glfMultiples) ||  $(BIN_DIR)/glfFlex --minMapQuality 0 --minDepth 1 --maxDepth 10000000 --uniformTsTv --smartFilter
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|-
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| VCFPILEUP || vcfPileup to generate rich per-site information || $(BIN_DIR)/vcfPileup
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|-
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| INFOCOLLECTOR || gather filtering statistics || $(BIN_DIR)/infoCollector
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|-
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| VCFMERGE || merge multiple VCFs separated by chunk of genomes || perl $(SCRIPT_DIR)/bams2vcfMerge.pl
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|-
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| VCFCOOKER || vcfCooker program for filtering || $(BIN_DIR)/vcfCooker
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|-
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| VCFSUMMARY || script to generate summary statistics of discovered sites || perl $(SCRIPT_DIR)/vcf-summary
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|-
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| VCFSPLIT || splits VCF into overlapping chunks for genotype refinement || perl $(SCRIPT_DIR)/vcfSplit.pl
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|-
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| VCFSPLIT4 || splits VCF into overlapping chunks for beagle version 4 genotype refinement || perl $(SCRIPT_DIR)/vcfSplit4.pl
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|-
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| VCF_SPLIT_CHROM || splits VCF into per chromosome VCFs || perl $(SCRIPT_DIR)/vcfSplitChr.pl
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|-
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| VCFPASTE || generate filtered genotype VCF || perl $(SCRIPT_DIR)/vcfPaste.p
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|-
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| BEAGLE || beagle program || java -Xmx4g -jar $(BIN_DIR)/beagle.20101226.jar seed=993478 gprobs=true niterations=50 lowmem=true
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|-
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| BEAGLE4 || beagle version 4 program || java -Xmx4g -jar $(BIN_DIR)/b4.r1219.jar seed=993478 gprobs=true
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|-
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| VCF2BEAGLE || convert VCF (with PL tag) into beagle input || perl $(SCRIPT_DIR)/vcf2Beagle.pl --PL
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|-
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| BEAGLE2VCF || convert beagle output to VCF || perl $(SCRIPT_DIR)/beagle2Vcf.pl
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|-
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| SVM_SCRIPT || SVM script || perl $(SCRIPT_DIR)/run_libsvm.pl
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|-
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| SVMLEARN || SVM program || $(BIN_DIR)/svm-train
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|-
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| SVMCLASSIFY || SVM program || $(BIN_DIR)/svm-predict
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|-
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| INVNORM || SVM program || $(BIN_DIR)/invNorm
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|-
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| THUNDER_STATES || flags for thunder states and weighted states || --states 400 --weightedStates 300
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|-
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| THUNDER || MaCH/Thunder genotype refinement step || $(BIN_DIR)/thunderVCF -r 30 --phase --dosage --compact --inputPhased $(THUNDER_STATES)
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|-
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| LIGATEVCF || ligate multiple phased VCFs while resolving the phase between VCFs || perl $(SCRIPT_DIR)/ligateVcf.pl
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|-
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| LIGATEVCF4 || ligate multiple phased VCFs while resolving the phase between VCFs || perl $(SCRIPT_DIR)/ligateVcf4.pl
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|-
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| VCFCAT || concatenate multiple VCFs || perl $(SCRIPT_DIR)/vcfCat.pl
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|-
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| BGZIP || bgzip program || $(BIN_DIR)/bgzip
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|-
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| TABIX || tabix program || $(BIN_DIR)/tabix
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|-
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| BAMUTIL || bam util program || $(BIN_DIR)/bam
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|-
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|}
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==== Options ====
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Configuration Key !! Program Description !! Default Value
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|-
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| || SLEEP_MULT || add sleep time prior to some steps; use only if too many steps are starting at the same time doing the same thing || 0
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|-
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| || REMOTE_PREFIX || add a prefix to paths when sending across to a remote machine ||
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|-
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|}
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==== Options ====
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{| class="wikitable" style="margin: 1em 1em 1em 0; background-color: #f9f9f9; border: 1px #aaa solid; border-collapse: collapse;" border="1"
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! Configuration Key !! Program Description !! Default Value
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|-
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| || SAMTOOLS_VIEW_FILTER ||  ||
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|-
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| || NOBAQ_SUBSTRINGS || skip the BAQ step if the BAM filename contains the specified space-separated substrings || SOLID
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|-
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| || MODEL_GLFSINGLE ||  ||
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|-
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| || MODEL_SKIP_DISCOVER ||  ||
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|-
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| || MODEL_AF_PRIOR ||  ||
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|-
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| || BAM_DEPEND ||  ||
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|-
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| || WGS_SVM ||  ||
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|-
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| || MAKE_OPTS ||  ||
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|-
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| || USE_SVMMODEL ||  ||
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|-
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| SVM_CUTOFF ||  ||
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|-
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| SVMMODEL ||  ||
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|-
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| || POS_SAMPLE ||  ||
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|-
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| || NEG_SAMPLE ||  ||
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|-
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| || KEEP_LOG ||  ||
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|-
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| || FILTER_ADDITIONAL ||  ||
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|-
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                        maxABL  => "FILTER_MAX_ABL",
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                        maxSTR  => "FILTER_MAX_STR",
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                        minSTR  => "FILTER_MIN_STR",
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                        winIndel => "FILTER_WIN_INDEL",
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                        maxSTZ  => "FILTER_MAX_STZ",
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                        minSTZ  => "FILTER_MIN_STZ",
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                        maxAOI  => "FILTER_MAX_AOI",
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                        minFIC  => "FILTER_MIN_FIC",
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                        maxCBR  => "FILTER_MAX_CBR",
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                        maxLQR  => "FILTER_MAX_LQR",
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                        minQual  => "FILTER_MIN_QUAL",
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                        minMQ    => "FILTER_MIN_MQ",
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                        maxMQ0  => "FILTER_MAX_MQ0",
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                        maxMQ30  => "FILTER_MAX_MQ30",
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                        maxAOZ  => "FILTER_MAX_AOZ",
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                        maxIOR  => "FILTER_MAX_IOR",
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|}
 
|}
Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/11888"

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