Difference between revisions of "GotCloud: Variant Calling Options"
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format (-end is optional): chr:start-end | format (-end is optional): chr:start-end | ||
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| + | | || UNIT_CHUNK || chunk size of SNP calling (GotCloud breaks up each chromosome into regions of this size) || 5000000 | ||
| + | |- | ||
| + | | || LD_NSNPS || chunk size (number of SNPs) of genotype refinement || 10000 | ||
| + | |- | ||
| + | | || LD_OVERLAP || overlapping # of SNPs between chunks for genotype refinement || 1000 | ||
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** see: [[GotCloud: FAQs#Targetted/Exome|GotCloud: FAQs->Targetted/Exome]] | ** see: [[GotCloud: FAQs#Targetted/Exome|GotCloud: FAQs->Targetted/Exome]] | ||
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=== Path Options === | === Path Options === | ||
Revision as of 14:29, 24 October 2014
Required Options
| Command-line Flag | Configuration Key | Value Description | Default Value |
|---|---|---|---|
| --outdir path | OUT_DIR | output directory | |
| --list/--bam_list/--bamlist file | BAM_LIST | path to the BAM List File | $(OUT_DIR)/bam.list |
| --numjobs # | number of jobs to run in parallel | 0 (generate Makefile of steps, but do not run) |
Common Options
| Common Options | |||
|---|---|---|---|
| Command-line Flag | Configuration Key | Value Description | Default Value |
| --conf file | configuration file to use | ||
Cluster Options
| Command-line Flag | Configuration Key | Value Description | Default Value |
|---|---|---|---|
| --batchtype type | BATCH_TYPE | name of cluster type | local |
| --batchopts opts | BATCH_OPTS | options to pass to the cluster command | |
| --copyglf path | COPY_GLF | path to copy glfs to before processing them (path local to remote nodes, maybe in /tmp) |
Test/Debug Options
| Command-line Flag | Configuration Key | Value Description | Default Value |
|---|---|---|---|
| --help | print help information | ||
| --test path | run the snpcall/ldrefine test and write output to the specified path | ||
| --verbose | Add additional messages when reading configuration |
Reference/Resource Files
- See GotCloud: Genetic Reference and Resource Files for reference/resource file configuration settings
Analysis Region Options
| Command-line Flag | Configuration Key | Value Description | Default Value |
|---|---|---|---|
| --chrs # # | CHRS | pace separated list of chromosomes to process | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X |
| --region #:#-# | call region - skip regions of chromosome outside of specified region
format (-end is optional): chr:start-end |
||
| UNIT_CHUNK | chunk size of SNP calling (GotCloud breaks up each chromosome into regions of this size) | 5000000 | |
| LD_NSNPS | chunk size (number of SNPs) of genotype refinement | 10000 | |
| LD_OVERLAP | overlapping # of SNPs between chunks for genotype refinement | 1000 |
Chromosome X Calling
For proper Chromosome X calling, it is recommended to specify a PED file with sex information:
| Configuration Key | Value Description |
|---|---|
| PED_INDEX | ped file containing sampleID (2nd column) and sex (5th column) |
Format of PED file:
familyID sampleID fatherID motherID sex
- Only
sampleIDandsexare used
Targeted/Exome Sequencing Settings
If you are running Targeted/Exome Sequencing, the user should specify:
| Configuration Key | Value Description |
|---|---|
| UNIFORM_TARGET_BED | Bed file of targeted regions (same bed for all samples) |
| MULTIPLE_TARGET_MAP | Filename of file mapping: sample id -> bed file of targeted regions
Each line of the file contains: [SM_ID] [TARGET_BED] |
| OFFSET_OFF_TARGET | Number of bases by which to extend the target region
(default is 0, do not extend the target region) |
| SAMTOOLS_VIEW_TARGET_ONLY | true: speeds up processing by excluding off-target regions initially when performing samtools view
false (default): off-target regions are not excluded when performing samtools view, but are excluded at a later step Warning: You may not want to set this to true due to it may:
|
Path Options
| Command-line Flag | Configuration Key | Value Description | Default Value |
|---|---|---|---|
| --makebasename name | MAKE_BASE_NAME | basename of the Makefile generated by GotCloud | umake |
| --bamprefix prefix | BAM_PREFIX | path to prepend to relative BAM file paths in the BAM list | |
| --refprefix prefix | REF_PREFIX | path to prepend to relative reference/resource file paths | |
| --baseprefix prefix | BASE_PREFIX | path to prepend to relative paths for the BAM list file, PED_INDEX, BAM (if BAM_PREFIX isn't specified), reference/resource files (if REF_PREFIX isn't specified) | |
| --refdir path | REF_DIR | value to use for REF_DIR key | $(GOTCLOUD_ROOT)/gotcloud.ref |
| --gotcloudroot path | GOTCLOUD_ROOT | specify to use a different directory for finding GotCloud bins/scripts | based on the location of the gotcloud/umake.pl script |
Validation Adjustment Options
| Command-line Flag | Configuration Key | Value Description | Default Value |
|---|---|---|---|
| --maxlocaljobs # | maximum # of jobs that can run if batchtype is local (to prevent accidentally starting jobs locally that were meant to be on a cluster) | 10 | |
| --ignoresmcheck | IGNORE_SM_CHECK | disable the validation that the Sample name in the BAM file matches the one in the BAM list file |
Miscellaneous Options
| Command-line Flag | Configuration Key | Value Description | Default Value |
|---|---|---|---|
| --nophonehome | disable phonehome in GotCloud and the tools it calls | ||
| BAMUTIL_THINNING | thinning parameter for bamUtil programs (will be set to 0 - if --nophonehome is specified) | --phoneHomeThinning 10 |
Directory Settings Options
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.
| Configuration Key | Value Description | Default Value |
|---|---|---|
| BAM_GLF_DIR | GLF outputs per BAM (if multiple BAMs per sample) (intermediate files) | glfs/bams |
| SM_GLF_DIR | GLF outputs per sample (intermediate files) | glfs/samples |
| VCF_DIR | unfiltered and filtered VCFs | vcfs |
| PVCF_DIR | vcfPileup results (intermediate files) | pvcfs |
| SPLIT_DIR | VCFs with PASS variants only & split into multiple files | split |
| BEAGLE_DIR | beagle output | beagle |
| SPLIT4_DIR | VCFs with PASS variants only & split into multiple files for running beagle4 | split4 |
| BEAGLE4_DIR | beagle version 4 output | beagle4 |
| THUNDER_DIR | thunder output | thunder |
| TARGET_DIR | directory to store target information when running with a BED file | target |
| GLF_INDEX | filename for index file needed for glfflex (file is created by GotCloud) | glfIndex.ped |
Tool Options
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.
Some tools have the options specified with the binary command, while others have them separate or hard coded
| Configuration Key | Program Description | Default Value |
|---|---|---|
| SAMTOOLS_FOR_PILEUP | samtools to use for pileup | $(BIN_DIR)/samtools-hybrid |
| SAMTOOLS_FOR_OTHERS | samtools to use for view and calmd | $(BIN_DIR)/samtools-hybrid |
| GLFMERGE | merge glf files when there are multiple BAMs per indvidual | $(BIN_DIR)/glfMerge |
| GLFFLEX | perform glf-based variant calling (replacement for glfMultiples) | $(BIN_DIR)/glfFlex --minMapQuality 0 --minDepth 1 --maxDepth 10000000 --uniformTsTv --smartFilter |
| VCFPILEUP | vcfPileup to generate rich per-site information | $(BIN_DIR)/vcfPileup |
| INFOCOLLECTOR | gather filtering statistics | $(BIN_DIR)/infoCollector |
| VCFMERGE | merge multiple VCFs separated by chunk of genomes | perl $(SCRIPT_DIR)/bams2vcfMerge.pl |
| VCFCOOKER | vcfCooker program for filtering | $(BIN_DIR)/vcfCooker |
| VCFSUMMARY | script to generate summary statistics of discovered sites | perl $(SCRIPT_DIR)/vcf-summary |
| VCFSPLIT | splits VCF into overlapping chunks for genotype refinement | perl $(SCRIPT_DIR)/vcfSplit.pl |
| VCFSPLIT4 | splits VCF into overlapping chunks for beagle version 4 genotype refinement | perl $(SCRIPT_DIR)/vcfSplit4.pl |
| VCF_SPLIT_CHROM | splits VCF into per chromosome VCFs | perl $(SCRIPT_DIR)/vcfSplitChr.pl |
| VCFPASTE | generate filtered genotype VCF | perl $(SCRIPT_DIR)/vcfPaste.p |
| BEAGLE | beagle program | java -Xmx4g -jar $(BIN_DIR)/beagle.20101226.jar seed=993478 gprobs=true niterations=50 lowmem=true |
| BEAGLE4 | beagle version 4 program | java -Xmx4g -jar $(BIN_DIR)/b4.r1219.jar seed=993478 gprobs=true |
| VCF2BEAGLE | convert VCF (with PL tag) into beagle input | perl $(SCRIPT_DIR)/vcf2Beagle.pl --PL |
| BEAGLE2VCF | convert beagle output to VCF | perl $(SCRIPT_DIR)/beagle2Vcf.pl |
| SVM_SCRIPT | SVM script | perl $(SCRIPT_DIR)/run_libsvm.pl |
| SVMLEARN | SVM program | $(BIN_DIR)/svm-train |
| SVMCLASSIFY | SVM program | $(BIN_DIR)/svm-predict |
| INVNORM | SVM program | $(BIN_DIR)/invNorm |
| THUNDER_STATES | flags for thunder states and weighted states | --states 400 --weightedStates 300 |
| THUNDER | MaCH/Thunder genotype refinement step | $(BIN_DIR)/thunderVCF -r 30 --phase --dosage --compact --inputPhased $(THUNDER_STATES) |
| LIGATEVCF | ligate multiple phased VCFs while resolving the phase between VCFs | perl $(SCRIPT_DIR)/ligateVcf.pl |
| LIGATEVCF4 | ligate multiple phased VCFs while resolving the phase between VCFs | perl $(SCRIPT_DIR)/ligateVcf4.pl |
| VCFCAT | concatenate multiple VCFs | perl $(SCRIPT_DIR)/vcfCat.pl |
| BGZIP | bgzip program | $(BIN_DIR)/bgzip |
| TABIX | tabix program | $(BIN_DIR)/tabix |
| BAMUTIL | bam util program | $(BIN_DIR)/bam |
Options
| Configuration Key | Program Description | Default Value | |
|---|---|---|---|
| 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 | |
| REMOTE_PREFIX | add a prefix to paths when sending across to a remote machine |
Options
maxABL => "FILTER_MAX_ABL", maxSTR => "FILTER_MAX_STR", minSTR => "FILTER_MIN_STR", winIndel => "FILTER_WIN_INDEL", maxSTZ => "FILTER_MAX_STZ", minSTZ => "FILTER_MIN_STZ", maxAOI => "FILTER_MAX_AOI", minFIC => "FILTER_MIN_FIC", maxCBR => "FILTER_MAX_CBR", maxLQR => "FILTER_MAX_LQR", minQual => "FILTER_MIN_QUAL", minMQ => "FILTER_MIN_MQ", maxMQ0 => "FILTER_MAX_MQ0", maxMQ30 => "FILTER_MAX_MQ30", maxAOZ => "FILTER_MAX_AOZ", maxIOR => "FILTER_MAX_IOR",| Configuration Key | Program Description | Default Value | |
|---|---|---|---|
| SAMTOOLS_VIEW_FILTER | |||
| NOBAQ_SUBSTRINGS | skip the BAQ step if the BAM filename contains the specified space-separated substrings | SOLID | |
| MODEL_GLFSINGLE | |||
| MODEL_SKIP_DISCOVER | |||
| MODEL_AF_PRIOR | |||
| BAM_DEPEND | |||
| WGS_SVM | |||
| MAKE_OPTS | |||
| USE_SVMMODEL | |||
| SVM_CUTOFF | |||
| SVMMODEL | |||
| POS_SAMPLE | |||
| NEG_SAMPLE | |||
| KEEP_LOG | |||
| FILTER_ADDITIONAL |
