GATK-Teaching
Category
Bioinformatics
Program On
Teaching
Version
3.4-0
Author / Distributor
Description
"The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size." More details are at GATK
Running Program
The last version of this application is at /usr/local/apps/eb/GATK/3.4-0-Java-1.8.0_144
To use this version, please load the module with
ml GATK/3.4-0-Java-1.8.0_144
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_GATK
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=GATK.%j.out
#SBATCH --error=GATK.%j.err
cd $SLURM_SUBMIT_DIR
ml GATK/3.4-0-Java-1.8.0_144
java -jar $EBROOTGATK/GenomeAnalysisTK.jar [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml GATK/3.4-0-Java-1.8.0_144 java -jar $EBROOTGATK/GenomeAnalysisTK.jar -h -------------------------------------------------------------------------------- The Genome Analysis Toolkit (GATK) v3.4-0-g7e26428, Compiled 2015/05/15 03:25:41 Copyright (c) 2010 The Broad Institute For support and documentation go to http://www.broadinstitute.org/gatk -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- usage: java -jar GenomeAnalysisTK.jar -T <analysis_type> [-args <arg_file>] [-I <input_file>] [--showFullBamList] [-rbs <read_buffer_size>] [-et <phone_home>] [-K <gatk_key>] [-tag <tag>] [-rf <read_filter>] [-drf <disable_read_filter>] [-L <intervals>] [-XL <excludeIntervals>] [-isr <interval_set_rule>] [-im <interval_merging>] [-ip <interval_padding>] [-R <reference_sequence>] [-ndrs] [-maxRuntime <maxRuntime>] [-maxRuntimeUnits <maxRuntimeUnits>] [-dt <downsampling_type>] [-dfrac <downsample_to_fraction>] [-dcov <downsample_to_coverage>] [-baq <baq>] [-baqGOP <baqGapOpenPenalty>] [-fixNDN] [-fixMisencodedQuals] [-allowPotentiallyMisencodedQuals] [-OQ] [-DBQ <defaultBaseQualities>] [-PF <performanceLog>] [-BQSR <BQSR>] [-qq <quantize_quals>] [-DIQ] [-EOQ] [-preserveQ <preserve_qscores_less_than>] [-globalQScorePrior <globalQScorePrior>] [-S <validation_strictness>] [-rpr] [-kpr] [-sample_rename_mapping_file <sample_rename_mapping_file>] [-U <unsafe>] [-disable_auto_index_creation_and_locking_when_reading_rods] [-sites_only] [-writeFullFormat] [-compress <bam_compression>] [-simplifyBAM] [--disable_bam_indexing] [--generate_md5] [-nt <num_threads>] [-nct <num_cpu_threads_per_data_thread>] [-mte] [-bfh <num_bam_file_handles>] [-rgbl <read_group_black_list>] [-ped <pedigree>] [-pedString <pedigreeString>] [-pedValidationType <pedigreeValidationType>] [-variant_index_type <variant_index_type>] [-variant_index_parameter <variant_index_parameter>] [-l <logging_level>] [-log <log_to_file>] [-h] [-version] -T,--analysis_type <analysis_type> Name of the tool to run -args,--arg_file <arg_file> Reads arguments from the specified file -I,--input_file <input_file> Input file containing sequence data (SAM or BAM) --showFullBamList Emit a log entry (level INFO) containing the full list of sequence data files to be included in the analysis (including files inside .bam.list files). -rbs,--read_buffer_size <read_buffer_size> Number of reads per SAM file to buffer in memory -et,--phone_home <phone_home> Run reporting mode (NO_ET|AWS| STDOUT) -K,--gatk_key <gatk_key> GATK key file required to run with -et NO_ET -tag,--tag <tag> Tag to identify this GATK run as part of a group of runs -rf,--read_filter <read_filter> Filters to apply to reads before analysis -drf,--disable_read_filter <disable_read_filter> Read filters to disable -L,--intervals <intervals> One or more genomic intervals over which to operate -XL,--excludeIntervals <excludeIntervals> One or more genomic intervals to exclude from processing -isr,--interval_set_rule <interval_set_rule> Set merging approach to use for combining interval inputs (UNION|INTERSECTION) -im,--interval_merging <interval_merging> Interval merging rule for abutting intervals (ALL| OVERLAPPING_ONLY) -ip,--interval_padding <interval_padding> Amount of padding (in bp) to add to each interval -R,--reference_sequence <reference_sequence> Reference sequence file -ndrs,--nonDeterministicRandomSeed Use a non-deterministic random seed -maxRuntime,--maxRuntime <maxRuntime> Stop execution cleanly as soon as maxRuntime has been reached -maxRuntimeUnits,--maxRuntimeUnits <maxRuntimeUnits> Unit of time used by maxRuntime (NANOSECONDS| MICROSECONDS|MILLISECONDS| SECONDS|MINUTES|HOURS|DAYS) -dt,--downsampling_type <downsampling_type> Type of read downsampling to employ at a given locus (NONE| ALL_READS|BY_SAMPLE) -dfrac,--downsample_to_fraction <downsample_to_fraction> Fraction of reads to downsample to -dcov,--downsample_to_coverage <downsample_to_coverage> Target coverage threshold for downsampling to coverage -baq,--baq <baq> Type of BAQ calculation to apply in the engine (OFF| CALCULATE_AS_NECESSARY| RECALCULATE) -baqGOP,--baqGapOpenPenalty <baqGapOpenPenalty> BAQ gap open penalty -fixNDN,--refactor_NDN_cigar_string Reduce NDN elements in CIGAR string -fixMisencodedQuals,--fix_misencoded_quality_scores Fix mis-encoded base quality scores -allowPotentiallyMisencodedQuals,--allow_potentially_misencoded_quality_scores Ignore warnings about base quality score encoding -OQ,--useOriginalQualities Use the base quality scores from the OQ tag -DBQ,--defaultBaseQualities <defaultBaseQualities> Assign a default base quality -PF,--performanceLog <performanceLog> Write GATK runtime performance log to this file -BQSR,--BQSR <BQSR> Input covariates table file for on-the-fly base quality score recalibration -qq,--quantize_quals <quantize_quals> Quantize quality scores to a given number of levels (with -BQSR) -DIQ,--disable_indel_quals Disable printing of base insertion and deletion tags (with -BQSR) -EOQ,--emit_original_quals Emit the OQ tag with the original base qualities (with -BQSR) -preserveQ,--preserve_qscores_less_than <preserve_qscores_less_than> Don't recalibrate bases with quality scores less than this threshold (with -BQSR) -globalQScorePrior,--globalQScorePrior <globalQScorePrior> Global Qscore Bayesian prior to use for BQSR -S,--validation_strictness <validation_strictness> How strict should we be with validation (STRICT|LENIENT| SILENT) -rpr,--remove_program_records Remove program records from the SAM header -kpr,--keep_program_records Keep program records in the SAM header -sample_rename_mapping_file,--sample_rename_mapping_file <sample_rename_mapping_file> Rename sample IDs on-the-fly at runtime using the provided mapping file -U,--unsafe <unsafe> Enable unsafe operations: nothing will be checked at runtime (ALLOW_N_CIGAR_READS| ALLOW_UNINDEXED_BAM| ALLOW_UNSET_BAM_SORT_ORDER| NO_READ_ORDER_VERIFICATION| ALLOW_SEQ_DICT_INCOMPATIBILITY| LENIENT_VCF_PROCESSING|ALL) d_locking_when_reading_rods,--disable_auto_index_creation_and_locking_when_reading_rods Disable both auto-generation of index files and index file locking -sites_only,--sites_only Just output sites without genotypes (i.e. only the first 8 columns of the VCF) -writeFullFormat,--never_trim_vcf_format_field Always output all the records in VCF FORMAT fields, even if some are missing -compress,--bam_compression <bam_compression> Compression level to use for writing BAM files (0 - 9, higher is more compressed) -simplifyBAM,--simplifyBAM If provided, output BAM files will be simplified to include just key reads for downstream variation discovery analyses (removing duplicates, PF-, non-primary reads), as well stripping all extended tags from the kept reads except the read group identifier --disable_bam_indexing Turn off on-the-fly creation of indices for output BAM files. --generate_md5 Enable on-the-fly creation of md5s for output BAM files. -nt,--num_threads <num_threads> Number of data threads to allocate to this analysis -nct,--num_cpu_threads_per_data_thread <num_cpu_threads_per_data_thread> Number of CPU threads to allocate per data thread -mte,--monitorThreadEfficiency Enable threading efficiency monitoring -bfh,--num_bam_file_handles <num_bam_file_handles> Total number of BAM file handles to keep open simultaneously -rgbl,--read_group_black_list <read_group_black_list> Exclude read groups based on tags -ped,--pedigree <pedigree> Pedigree files for samples -pedString,--pedigreeString <pedigreeString> Pedigree string for samples -pedValidationType,--pedigreeValidationType <pedigreeValidationType> Validation strictness for pedigree information (STRICT| SILENT) -variant_index_type,--variant_index_type <variant_index_type> Type of IndexCreator to use for VCF/BCF indices (DYNAMIC_SEEK|DYNAMIC_SIZE| LINEAR|INTERVAL) -variant_index_parameter,--variant_index_parameter <variant_index_parameter> Parameter to pass to the VCF/BCF IndexCreator -l,--logging_level <logging_level> Set the minimum level of logging -log,--log_to_file <log_to_file> Set the logging location -h,--help Generate the help message -version,--version Output version information annotator VariantAnnotator Annotate variant calls with context information beagle BeagleOutputToVCF Takes files produced by Beagle imputation engine and creates a vcf with modified annotations. ProduceBeagleInput Converts the input VCF into a format accepted by the Beagle imputation/analysis program. VariantsToBeagleUnphased Produces an input file to Beagle imputation engine, listing unphased, hard-called genotypes for a single sample in input variant file. bqsr AnalyzeCovariates Create plots to visualize base recalibration results <p/> This tool generates plots for visualizing the quality of a recalibration run. BaseRecalibrator Generate base recalibration table to compensate for systematic errors coverage CallableLoci Collect statistics on callable, uncallable, poorly mapped, and other parts of the genome CompareCallableLoci Compare callability statistics DepthOfCoverage Assess sequence coverage by a wide array of metrics, partitioned by sample, read group, or library GCContentByInterval Calculates the GC content of the reference sequence for each interval diagnosetargets DiagnoseTargets Analyze coverage distribution and validate read mates per interval and per sample diagnostics BaseCoverageDistribution Evaluate coverage distribution per base CoveredByNSamplesSites Report well-covered intervals ErrorRatePerCycle Compute the read error rate per position FindCoveredIntervals Outputs a list of intervals that are covered above a given threshold ReadGroupProperties Collect statistics about read groups and their properties ReadLengthDistribution Collect read length statistics examples GATKPaperGenotyper A simple Bayesian genotyper, that outputs a text based call format. fasta FastaAlternateReferenceMaker Generate an alternative reference sequence over the specified interval FastaReferenceMaker Create a subset of a FASTA reference sequence FastaStats Calculate basic statistics about the reference sequence itself filters VariantFiltration Filter variant calls based on INFO and FORMAT annotations genotyper UnifiedGenotyper Call SNPs and indels on a per-locus basis haplotypecaller HaplotypeCaller Call SNPs and indels simultaneously via local re-assembly of haplotypes in an active region HaplotypeResolver Haplotype-based resolution of variants in separate callsets. indels IndelRealigner Perform local realignment of reads around indels LeftAlignIndels Left-align indels within reads in a bam file RealignerTargetCreator Define intervals to target for local realignment missing QualifyMissingIntervals Collect quality metrics for a set of intervals phasing PhaseByTransmission Compute the most likely genotype combination and phasing for trios and parent/child pairs ReadBackedPhasing Annotate physical phasing information qc CheckPileup Compare GATK's internal pileup to a reference Samtools pileup CountBases Count the number of bases in a set of reads CountIntervals Count contiguous regions in an interval list CountLoci Count the total number of covered loci CountMales Count the number of reads seen from male samples CountReadEvents Count the number of read events CountReads Count the number of reads CountRODs Count the number of ROD objects encountered CountRODsByRef Count the number of ROD objects encountered along the reference CountTerminusEvent Count the number of reads ending in insertions, deletions or soft-clips ErrorThrowing A walker that simply throws errors. FlagStat Collect statistics about sequence reads based on their SAM flags Pileup Print read alignments in Pileup-style format PrintRODs Print out all of the RODs in the input data set QCRef Quality control for the reference fasta ReadClippingStats Collect read clipping statistics readutils ClipReads Read clipping based on quality, position or sequence matching PrintReads Write out sequence read data (for filtering, merging, subsetting etc) ReadAdaptorTrimmer Utility tool to blindly strip base adaptors SplitSamFile Split a BAM file by sample rnaseq ASEReadCounter Calculate read counts per allele for allele-specific expression analysis SplitNCigarReads Splits reads that contain Ns in their CIGAR string simulatereads SimulateReadsForVariants Generate simulated reads for variants validation GenotypeAndValidate Genotype and validate a dataset and the calls of another dataset using the Unified Genotyper validationsiteselector ValidationSiteSelector Randomly select variant records according to specified options varianteval VariantEval General-purpose tool for variant evaluation (% in dbSNP, genotype concordance, Ti/Tv ratios, and a lot more) variantrecalibration ApplyRecalibration Apply a score cutoff to filter variants based on a recalibration table VariantRecalibrator Build a recalibration model to score variant quality for filtering purposes variantutils CalculateGenotypePosteriors Calculate genotype posterior likelihoods given panel data CombineGVCFs Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file CombineVariants Combine variant records from different sources FilterLiftedVariants Filters a lifted-over VCF file for reference bases that have been changed GenotypeConcordance Genotype concordance between two callsets GenotypeGVCFs Perform joint genotyping on gVCF files produced by HaplotypeCaller LeftAlignAndTrimVariants Left-align indels in a variant callset LiftoverVariants Lifts a VCF file over from one build to another RandomlySplitVariants Randomly split variants into different sets RegenotypeVariants Regenotypes the variants from a VCF containing PLs or GLs. SelectHeaders Selects headers from a VCF source SelectVariants Select a subset of variants from a larger callset ValidateVariants Validate a VCF file with an extra strict set of criteria VariantsToAllelicPrimitives Simplify multi-nucleotide variants (MNPs) into more basic/primitive alleles. VariantsToBinaryPed Convert VCF to binary pedigree file VariantsToTable Extract specific fields from a VCF file to a tab-delimited table VariantsToVCF Convert variants from other file formats to VCF format VariantValidationAssessor Annotate a validation VCF with QC metrics
Installation
Source code is obtained from GATK
System
64-bit Linux