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genotypeGVCFs vcf files empty, only the header

I'm running genotypeGVCFs on GATK 3.7/3.8, I tried both, but I'm only getting headers on the vcf files.
I ran

java -XX:ParallelGCThreads=4 -Xmx15g -jar GenomeAnalysisTKjar -T GenotypeGVCFs -R ref.fa -G none -L Chr29 -V AFR.Chr29.g.vcf -o AFR.Chr29.vcf.gz --heterozygosity 0.0015 --disable_auto_index_creation_and_locking_when_reading_rods

and this is what I get:

INFO 08:43:37,637 HelpFormatter - ----------------------------------------------------------------------------------
INFO 08:43:37,639 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50
INFO 08:43:37,640 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
INFO 08:43:37,640 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
INFO 08:43:37,640 HelpFormatter - [Mon Aug 14 08:43:37 SAST 2017] Executing on Linux 2.6.32-220.el6.x86_64 amd64
INFO 08:43:37,640 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_51-b16
INFO 08:43:37,644 HelpFormatter - Program Args: -T GenotypeGVCFs -R ref.fa -G none -L Chr29 -V AFR.Chr29.g.vcf -o AFR.Chr29.vcf.gz --heterozygosity 0.0015 --disable_auto_index_creation_and_locking_when_reading_rods
INFO 08:43:37,649 HelpFormatter - Executing as shoni@cn13 on Linux 2.6.32-220.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_51-b16.
INFO 08:43:37,649 HelpFormatter - Date/Time: 2017/08/14 08:43:37
INFO 08:43:37,650 HelpFormatter - ----------------------------------------------------------------------------------
INFO 08:43:37,650 HelpFormatter - ----------------------------------------------------------------------------------
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:GenomeAnalysisTK jar!/META-INF/log4j-provider.properties
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
INFO 08:43:37,798 GenomeAnalysisEngine - Deflater: IntelDeflater
INFO 08:43:37,799 GenomeAnalysisEngine - Inflater: IntelInflater
INFO 08:43:37,799 GenomeAnalysisEngine - Strictness is SILENT
INFO 08:43:39,188 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO 08:43:40,494 IntervalUtils - Processing 51505224 bp from intervals
INFO 08:43:40,525 MicroScheduler - Running the GATK in parallel mode with 10 total threads, 1 CPU thread(s) for each of 10 data thread(s), of 16 processors available on this machine
INFO 08:43:40,601 GenomeAnalysisEngine - Preparing for traversal
INFO 08:43:40,602 GenomeAnalysisEngine - Done preparing for traversal
INFO 08:43:40,603 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO 08:43:40,603 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 08:43:40,603 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 08:43:40,876 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files
INFO 08:44:07,152 ProgressMeter - done 5.1505224E7 26.0 s 0.0 s 100.0% 26.0 s 0.0 s
INFO 08:44:07,153 ProgressMeter - Total runtime 26.55 secs, 0.44 min, 0.01 hours

GATK 3.7 doesn't give an error, but also gives empty vcf file

Please help

Shoni

Tagged:

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @shonys
    Hi,

    Can you try with the very latest nightly build? Also, please post some example GVCF variant records that do not show up in the final VCF.

    Thanks,
    Sheila

  • Hi Sheila. I tried the latest nightly build, but i'm still getting the same results.

    fileformat=VCFv4.2

    ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">

    FILTER=<ID=LowQual,Description="Low quality">

    FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">

    FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">

    FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">

    FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">

    FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">

    FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">

    FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)">

    FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">

    GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=nightly-2017-11-14-1,Date="Tue Nov 14 12:29:36 SAST 2017",Epoch=1510655376433,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/scratch/sysusers/shoni/REF_GENOME/umd_3_1_reference_1000_bull_genomes.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=AFR.Chr2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant2 source=DRA.Chr2.g.vcf)]), (RodBindingCollection [(RodBinding name=variant3 source=NGI.Chr2.g.vcf)])] out=/scratch/sysusers/shoni/seqdata/rerun_2017/cohort.Chr2.vcf includeNonVariantSites=false uniquifySamples=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=10.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=2 annotation=[] group=[StandardAnnotation] dbsnp=(RodBinding name= source=UNBOUND) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

    GATKCommandLine.HaplotypeCaller=<ID=HaplotypeCaller,Version=3.8-0-ge9d806836,Date="Wed Nov 08 18:21:26 SAST 2017",Epoch=1510158086754,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[AFR.realigned.recalibrated.bam] showFullBamList=false read_buffer_size=null read_filter=[] disable_read_filter=[] intervals=[Chr2] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/scratch/sysusers/shoni/REF_GENOME/umd_3_1_reference_1000_bull_genomes.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=500 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=4 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false likelihoodCalculationEngine=PairHMM heterogeneousKmerSizeResolution=COMBO_MIN dbsnp=(RodBinding name= source=UNBOUND) dontTrimActiveRegions=false maxDiscARExtension=25 maxGGAARExtension=300 paddingAroundIndels=150 paddingAroundSNPs=20 comp=[] annotation=[StrandBiasBySample] excludeAnnotation=[ChromosomeCounts, FisherStrand, StrandOddsRatio, QualByDepth] group=[StandardAnnotation, StandardHCAnnotation] debug=false useFilteredReadsForAnnotations=false emitRefConfidence=GVCF bamOutput=null bamWriterType=CALLED_HAPLOTYPES emitDroppedReads=false disableOptimizations=false annotateNDA=false useNewAFCalculator=false heterozygosity=0.001 indel_heterozygosity=1.25E-4 heterozygosity_stdev=0.01 standard_min_confidence_threshold_for_calling=-0.0 standard_min_confidence_threshold_for_emitting=30.0 max_alternate_alleles=6 max_genotype_count=1024 max_num_PL_values=100 input_prior=[] sample_ploidy=20 genotyping_mode=DISCOVERY alleles=(RodBinding name= source=UNBOUND) contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=null exactcallslog=null output_mode=EMIT_VARIANTS_ONLY allSitePLs=true gcpHMM=10 pair_hmm_implementation=FASTEST_AVAILABLE phredScaledGlobalReadMismappingRate=45 noFpga=false nativePairHmmThreads=1 useDoublePrecision=false sample_name=null kmerSize=[10, 25] dontIncreaseKmerSizesForCycles=false allowNonUniqueKmersInRef=false numPruningSamples=1 recoverDanglingHeads=false doNotRecoverDanglingBranches=false minDanglingBranchLength=4 consensus=false maxNumHaplotypesInPopulation=128 errorCorrectKmers=false minPruning=2 debugGraphTransformations=false allowCyclesInKmerGraphToGeneratePaths=false graphOutput=null kmerLengthForReadErrorCorrection=25 minObservationsForKmerToBeSolid=20 GVCFGQBands=[1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 70, 80, 90, 99] indelSizeToEliminateInRefModel=10 min_base_quality_score=10 includeUmappedReads=false useAllelesTrigger=false doNotRunPhysicalPhasing=true keepRG=null justDetermineActiveRegions=false dontGenotype=false dontUseSoftClippedBases=false captureAssemblyFailureBAM=false errorCorrectReads=false pcr_indel_model=CONSERVATIVE maxReadsInRegionPerSample=10000 minReadsPerAlignmentStart=10 mergeVariantsViaLD=false activityProfileOut=null activeRegionOut=null activeRegionIn=null activeRegionExtension=null forceActive=false activeRegionMaxSize=null bandPassSigma=null maxReadsInMemoryPerSample=30000 maxTotalReadsInMemory=10000000 maxProbPropagationDistance=50 activeProbabilityThreshold=0.002 min_mapping_quality_score=20 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">

    INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">

    INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">

    INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">

    INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

    INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">

    INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">

    INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">

    INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">

    INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity">

    INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">

    INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">

    INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">

    INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">

    INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">

    INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">

    INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">

    INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">

    INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality">

    INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">

    INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias">

    reference=file:///scratch/sysusers/shoni/REF_GENOME/umd_3_1_reference_1000_bull_genomes.fa

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AFR DRA NGI

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @shonys
    Hi,

    Can you post some variant records from AFR.Chr29.g.vcf? Are there any variant sites or only hom-ref blocks present?

    Thanks,
    Sheila

  • Hi Sheila
    please find the first records of the gvcf file as requested

    CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AFR

    Chr29 1 . G . . END=9 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:11:2:10:0,2,5,7,10,12,15
    ,19,22,26,30,35,40,45,52,60,70,82,99,128,276
    Chr29 10 . C . . END=10 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:13:3:13:0,3,6,9,13,16,20
    ,24,29,34,39,45,52,59,68,78,90,106,129,167,359
    Chr29 11 . C . . END=11 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:13:0:13:0,0,0,0,0,0,0,0,
    0,4,8,13,19,26,33,42,54,68,89,123,298
    Chr29 12 . C . . END=28 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:13:3:13:0,3,6,9,13,16,20
    ,24,29,34,39,45,51,59,67,78,90,106,128,165,343
    Chr29 29 . G . . END=32 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:16:4:16:0,4,7,11,15,20,2
    5,30,35,41,48,55,63,73,83,96,111,131,159,206,449
    Chr29 33 . C . . END=33 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:14:3:14:0,3,6,10,14,17,2
    2,26,31,36,42,48,56,64,73,84,97,115,139,180,387
    Chr29 34 . G . . END=35 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:16:4:16:0,4,7,11,15,20,2
    5,30,35,41,48,55,63,72,83,95,110,129,156,200,353
    Chr29 36 . T . . END=36 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:14:3:14:0,3,6,10,14,17,2
    2,26,31,36,42,48,56,64,73,84,97,115,139,180,386
    Chr29 37 . C . . END=42 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:16:4:16:0,4,7,11,15,20,2
    5,30,35,41,48,55,63,73,83,96,111,131,159,205,436
    Chr29 43 . C . . END=43 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:16:0:16:0,0,0,0,0,0,0,2,
    6,12,17,24,31,39,49,60,74,93,118,162,378
    Chr29 44 . C . . END=48 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:16:4:16:0,4,7,11,15,20,2
    5,30,35,41,48,55,63,73,83,96,111,131,158,205,444
    Chr29 49 . A . . END=49 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:14:3:14:0,3,6,10,14,17,2
    2,26,31,36,42,48,56,64,73,84,97,115,139,180,407
    Chr29 50 . A . . END=54 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:16:4:16:0,4,7,11,15,20,2
    5,30,35,41,48,55,63,73,83,96,111,131,159,205,436
    Chr29 55 . G . . END=55 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:14:3:14:0,3,6,10,14,17,2
    2,26,31,36,42,48,56,64,73,84,97,115,139,180,396
    Chr29 56 . A . . END=61 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:17:4:16:0,4,7,11,15,20,2
    5,30,35,41,48,55,63,73,83,96,111,131,159,205,436
    Chr29 62 . T . . END=62 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:15:3:15:0,3,7,11,15,19,2
    3,28,33,39,45,52,59,68,78,90,104,123,149,193,407
    Chr29 63 . G . . END=68 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:17:4:17:0,4,8,12,16,21,2
    6,32,38,44,51,59,67,77,88,102,118,139,168,218,448
    Chr29 69 . C . . END=69 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:17:0:17:0,0,0,0,0,0,0,3,
    8,14,20,27,34,43,53,66,80,100,126,171,373
    Chr29 70 . A . . END=74 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:17:4:17:0,4,7,11,16,20,2
    5,30,35,42,48,55,64,73,84,96,112,132,160,208,457
    Chr29 75 . C . . END=78 GT:DP:GQ
    :MIN_DP:PL 0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0/0:17:3:17:0,3,7,11,15,19,2

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @shonys
    Hi,

    Notice there are no alternate alleles present in the genotypes. A lot of the GQs look low, but in the end, the most likely genotype is the hom-ref genotype. The final VCF contains no variants, because the GVCFs do not have any variant sites.

    What kind of data are you working with and what is your end goal?

    Thanks,
    Sheila

  • Hi, Im working on cattle dataset for SNP discovery. I did call variants before on the same dataset. I only put the ploidy option which I didn't include before since i'm analysing pooled data. What could be the problem?

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @shonys
    Hi,

    Did you get variants in your final VCF before? If so, what did you use to call variants? Can you post an IGV screenshot of a region in your BAM file that you think should get variants called?

    Thanks,
    Sheila

  • yes, using GATK 3.5. I dont understand why the latest versions are failing to give variants. Have someone ever called variants on pooled data and experienced the same? The only parameter that I added is -ploidy. Unfortunately I dont have IGV.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator

    @shonys
    Hi,

    That is odd. So, you ran 3.5 with default ploidy of 2 and get variants, but when you increase the ploidy in 3.8, you get no variants? Can you test GATK4 latest beta here? I may need you to submit a bug report.

    -Sheila

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