GATK-Teaching
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Category
Bioinformatics
Program On
Teaching
Version
3.8-0
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/3.8-0-Java-1.8.0_144
To use this version, please load the module with
ml GATK/3.8-0-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/3.8-0-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/3.8-0-Java-1.8.0_144
java -jar $EBROOTGATK/GenomeAnalysisTK.jar -h
----------------------------------------------------------------------------------
The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
Copyright (c) 2010-2016 The Broad Institute
For support and documentation go to https://software.broadinstitute.org/gatk
[Wed Aug 15 15:22:45 EDT 2018] Executing on Linux 3.10.0-862.9.1.el7.x86_64 amd64
Java HotSpot(TM) 64-Bit Server VM 1.8.0_144-b01
----------------------------------------------------------------------------------
----------------------------------------------------------------------------------
usage: java -jar GenomeAnalysisTK.jar -T <analysis_type> [-args <arg_file>] [-I <input_file>] [--showFullBamList] [-rbs
<read_buffer_size>] [-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>] [-SQQ <static_quantized_quals>] [-DIQ] [-EOQ] [-preserveQ <preserve_qscores_less_than>]
[-globalQScorePrior <globalQScorePrior>] [-secondsBetweenProgressUpdates <secondsBetweenProgressUpdates>] [-S
<validation_strictness>] [-rpr] [-kpr] [-sample_rename_mapping_file <sample_rename_mapping_file>] [-U <unsafe>]
[-jdk_deflater] [-jdk_inflater] [-disable_auto_index_creation_and_locking_when_reading_rods] [-no_cmdline_in_header]
[-sites_only] [-writeFullFormat] [-compress <bam_compression>] [-simplifyBAM] [--disable_bam_indexing] [--generate_md5]
[-nt <num_threads>] [-nct <num_cpu_threads_per_data_thread>] [-mte] [-rgbl <read_group_black_list>] [-ped <pedigree>]
[-pedString <pedigreeString>] [-pedValidationType <pedigreeValidationType>] [-variant_index_type <variant_index_type>]
[-variant_index_parameter <variant_index_parameter>] [-ref_win_stop <reference_window_stop>] [-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 (BAM or CRAM)
--showFullBamList Emit list of input BAM/CRAM
files to log
-rbs,--read_buffer_size <read_buffer_size> Number of reads per SAM file
to buffer in memory
-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)
-SQQ,--static_quantized_quals <static_quantized_quals> Use static quantized 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
-secondsBetweenProgressUpdates,--secondsBetweenProgressUpdates Time interval for process
<secondsBetweenProgressUpdates> meter information output (in
seconds)
-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)
-jdk_deflater,--use_jdk_deflater Use the JDK Deflater instead
of the IntelDeflater for
writing BAMs
-jdk_inflater,--use_jdk_inflater Use the JDK Inflater instead
of the IntelInflater for
reading BAMs
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
-no_cmdline_in_header,--no_cmdline_in_header Don't include the command line
in output VCF headers
-sites_only,--sites_only Output sites-only 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 Strip down read content and
tags
--disable_bam_indexing Turn off on-the-fly creation
of indices for output BAM/CRAM
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
-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 (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
-ref_win_stop,--reference_window_stop <reference_window_stop> Reference window stop
-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
bqsr
AnalyzeCovariates Create plots to visualize base recalibration results
BaseRecalibrator Detect systematic errors in base quality scores
cancer
AssignSomaticStatus Assigns somatic status to a set of calls
contamination
AnnotatePopulationAFWalker Given a input VCF representing a collection of populations, split the input into each
population, and annotate each record with population allele frequencies
ContEst Estimate cross-sample contamination
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
ErrorRatePerCycle Compute the read error rate per position
FindCoveredIntervals Outputs a list of intervals that are covered to or above a given threshold
ReadGroupProperties Collect statistics about read groups and their properties
ReadLengthDistribution Collect read length statistics
diffengine
DiffObjects A generic engine for comparing tree-structured objects
examples
GATKPaperGenotyper Simple Bayesian genotyper used in the original GATK paper
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 germline SNPs and indels via local re-assembly of haplotypes
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
m2
MuTect2 Call somatic SNPs and indels via local re-assembly of haplotypes
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)
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
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
GenotypeConcordance Genotype concordance between two callsets
GenotypeGVCFs Perform joint genotyping on gVCF files produced by HaplotypeCaller
LeftAlignAndTrimVariants Left-align indels in a variant callset
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
Installation
Source code is obtained from GATK
System
64-bit Linux