GATK IndelGenotyperV2 error

Question

[bruseq]

Hello

I m using gatk-IndelGenotyperV2 for indel, but getting error that:

ERROR MESSAGE: Invalid command line: Malformed walker argument: Could not find walker with name: IndelGenotyperV2.

Can anyone please guide me how to solve this error, this IndelGenotyperV2 package is not present in GenomeAnalysisTK.jar file. Please guide to solve this error.

Thank you,

Divya

[Ray Lee]

my help is like, Have I downloaded the wrong package ?

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The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
Copyright (c) 2010-2016 The Broad Institute
For support and documentation go to https://software.broadinstitute.org/gatk
[Tue Apr 04 01:22:53 CST 2017] Executing on Linux 4.4.0-59-generic amd64
OpenJDK 64-Bit Server VM 9-internal+0-2016-04-14-195246.buildd.src
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
usage: java -jar GenomeAnalysisTK.jar -T <analysis_type> [-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>] 
       [-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
 -I,--input_file <input_file>                                                             Input file containing sequence 
                                                                                          data (BAM or CRAM)
 --showFullBamList                                                                        Emit list of input BAM/CRAM 
                                                                                          files to log

[Pierre Lindenbaum]

don't use java OpenJDK 64-Bit http://gatkforums.broadinstitute.org/gatk/discussion/1852/what-are-the-prerequisites-for-running-gatk

Note that at this time we only support the Sun/Oracle Java JDK; OpenJDK is not supported.

Answer 1

[Pierre Lindenbaum]

there is no such tool "IndelGenotyperV2" ni gatk 3.7. This tool is deprecated: http://gatkforums.broadinstitute.org/gatk/discussion/comment/19452/#Comment_19452

in 3.7, the available tools are:

java -jar GenomeAnalysisTK.jar  -h

 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
 (...)