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Unified Genotyper Allele Depth (AD) filed for samples


I found some strange entries for indels in my VCF file created by the Unified Genotyper. For example:

4 184513470 . TC T 4009 PASS AC=4;AF=0.250;AN=16;BaseQRankSum=1.972;DP=1315;DS;FS=3.466;HaplotypeScore=537.6937;MLEAC=4;MLEAF=0.250;MQ=52.55;MQ0=0;MQRankSum=-10.581;QD=4.55;ReadPosRankSum=-10.128;SB=-3.500e+01;set=variant2 GT:AD:DP:GQ:PL 0/1:230,0:239:99:282,0,5011 0/0:92,0:95:99:0,133,2435

The first sample has genotype 0/1 with a good GQ value. However, according the allele depth field, there is no read supporting the deletion. When I look at the reads using the IGV, I find some reads supporting the deletion for the first sample (and even some for the second one).

Moreover, when I looked at the AD values for SNPs, I noticed the the sum of all AD values is much less than the coverage shown in the IGV. I filtered duplicated reads in the IGV.

Can someone please give an explanation? This link
explains the difference between AD and DP, but does not help in my case.

Best greetings,


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Hans, what version of the GATK are you using?

  • Sorry, I forgot to give the version number. It is "The Genome Analysis Toolkit (GATK) v2.1-8-g5efb575, Compiled 2012/08/30 14:22:17"

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Ah, you'll need to upgrade to the latest version. The issue you're having has been fixed.

  • OK, I will try the new version. Thanks!

  • Hi, I got the same entries with GATK-lite. Did you solve the problem with the latest version. If so, which version you did. Thanks.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @dolsemtl, I recommend you use the very latest version (currently 2.3-9).

  • alimanaliman Oxford, UKMember

    Hi, using GATK 2.3-9 I'm finding that the allele depths (AD field in calldata) for deletions called with the UnifiedGenotyper (ploidy=1) are zero or very low for both ref and alt where there are clearly many reads supporting one or the other allele. Here's an example:

    Pf3D7_04_v3 99839 . CTATATATATATATATA C 55455.68 PASS AC=13;AF=0.591;AN=22;BaseCounts=75,1255,0,1;BaseQRankSum=-3.665;DP=1343;FS=0.0;HRun=0;HaplotypeScore=65.1358;IndelType=DEL.NOVEL_10orMore.;LowMQ=0.0067,0.0067,1343.0;MLEAC=13;MLEAF=0.591;MQ=53.45;MQ0=0;MQ0Fraction=0.0067;MQRankSum=-2.757;QD=61.89;RPA=19,11;RU=TA;ReadPosRankSum=1.839;SB=-23010.0;STR;RegionType=Conserved;DPSoftClipped=130;DPMateSameStrand=0;DPFaceAway=0;DPAll=1158;DPProperPair=1153;DPMateOtherChrom=2;DPDuplicate=0;DPMateUnmapped=3;DPNormedByGC=0.871987951807;DPNormed=0.535120147874;DPPercentile=15;DPPercentileByGC=38;StdTlen=299;MeanTlen=26;RMSTlen=300;SoftClippingBias=7;UQ=45;GC100=7.0;GC300=11.0;GC500=14.0;HProx5=24;HProx10=275;HProx15=485;DPProperPairFraction=0.9957;DPMateUnmappedFraction=0.0026;DPMateOtherChromFraction=0.0017;DPMateSameStrandFraction=0.0;DPFaceAwayFraction=0.0;DPSoftClippedFraction=0.1123;DPDuplicateFraction=0.0;DPBiasStudent=9;DPBiasWelch=9;DPBiasRankSum=8 GT:AD:DP:GQ:MLPSAC:MLPSAF:MQ0:PL 1:0,1:62:99:1:1.0:0:3233,0 0:0,0:53:99:0:0.0:0:0,4619 0:0,0:75:99:0:0.0:0:0,6389 0:0,0:51:99:0:0.0:0:0,3802 1:0,0:85:99:1:1.0:0:6233,0 0:0,0:82:99:0:0.0:0:0,8012 1:0,2:117:99:1:1.0:1:6877,0 0:0,0:12:99:0:0.0:0:0,586 1:0,2:67:99:1:1.0:0:4769,0 1:0,1:34:99:1:1.0:0:2814,0 0:0,0:56:99:0:0.0:1:0,5989 0:0,0:15:99:0:0.0:0:0,1766 1:0,1:62:99:1:1.0:1:3643,0 1:0,2:50:99:1:1.0:2:2681,0 1:0,4:79:99:1:1.0:1:5223,0 0:0,0:33:99:0:0.0:0:0,2154 0:0,0:65:99:0:0.0:1:0,6721 1:0,0:25:99:1:1.0:0:2167,0 1:0,1:57:99:1:1.0:0:4339,0 1:0,1:116:99:1:1.0:2:7482,0 1:0,4:77:99:1:1.0:0:4884,0 1:0,1:49:99:1:1.0:0:1201,0

    Here's the VCF header:

    UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[./data/3d7_v3/bwa_n0.01_k4_l32/alignment_realigned_merged/3d7_hb3.bam] read_buffer_size=null phone_home=STANDARD gatk_key=null tag=NA read_filter=[] intervals=[Pf3D7_04_v3] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=./data/genome/sanger/version3/September_2012/Pf3D7_v3.fa nonDeterministicRandomSeed=false disableRandomization=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=NONE downsample_to_fraction=null downsample_to_coverage=null use_legacy_downsampler=false baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null 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 logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=INDEL pcr_error_rate=1.0E-4 computeSLOD=true annotateNDA=false pair_hmm_implementation=ORIGINAL min_base_quality_score=17 max_deletion_fraction=0.05 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=1 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 p_nonref_model=EXACT_GENERAL_PLOIDY contamination_fraction_to_filter=0.0 logRemovedReadsFromContaminationFiltering=null exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] debug_file=null metrics_file=null annotation=[IndelType, BaseCounts, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest, DepthOfCoverage, DepthPerAlleleBySample, FisherStrand, HaplotypeScore, HomopolymerRun, LowMQ, MappingQualityRankSumTest, MappingQualityZero, MappingQualityZeroBySample, MappingQualityZeroFraction, QualByDepth, RMSMappingQuality, ReadPosRankSumTest, SampleList, SpanningDeletions] excludeAnnotation=[] filter_mismatching_base_and_quals=false"



  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi Alistair,

    There's not much we can say about this without seeing some pileups or other data. There's a lot of things that could explain why the supporting reads you see aren't being counted. I recommend you check out this article:

    If you still think the AD numbers are incorrect, take an IGV screenshot of your example region and show us which reads you think aren't being counted.

  • celzingacelzinga Member
    edited March 2013


    I'm seeing a similar problem (using 2.3.9), and I'm noticing a pattern: it seems only to occur when there is a SNP at the same location for one of the samples in the UG run. Oddly enough, it happens regardless of whether I'm using -glm BOTH or -glm INDEL. If I omit the sample(s) that contain the SNP, then the insertion/deletion reads do get counted in AD.

    Here's a part of the VCF from a UG run that included a sample with a SNP at the location (the sample with the SNP is not shown in the snippet below):
    6 110053824 . G T 2757.13 . AC=1;AF=0.031;AN=32;BaseQRankSum=-14.015;DP=3471;Dels=0.00;FS=48.970;HaplotypeScore=191.7272;InbreedingCoeff=-0.0360;MLEAC=1;MLEAF=0.031;MQ=56.65;MQ0=2;MQRankSum=3.472;QD=11.03;ReadPosRankSum=-6.390 GT:AD:DP:GQ:PL 0/0:236,14:250:99:0,526,6571
    6 110053824 rs150311668 G GT 371313.22 . AC=29;AF=0.906;AN=32;DB;DP=3471;FS=2.505;HaplotypeScore=281.0531;InbreedingCoeff=-0.1056;MLEAC=29;MLEAF=0.906;MQ=56.65;MQ0=0;QD=106.98;RPA=13,14;RU=T;STR GT:AD:DP:GQ:PL 1/1:0,0:250:99:7049,428,0

    Then, when I omitted the sample with a SNP at that location for the UG run, I get the insertion count in AD (using the same UG settings):
    6 110053824 rs150311668 G GT 32729.73 . AC=2;AF=1.00;AN=2;BaseQRankSum=-0.234;DB;DP=250;FS=4.614;HaplotypeScore=325.8291;MLEAC=2;MLEAF=1.00;MQ=57.69;MQ0=0;MQRankSum=1.010;QD=130.92;RPA=13,14;RU=T;ReadPosRankSum=-0.688;STR GT:AD:DP:GQ:PL 1/1:10,212:250:99:6965,379,0

    I had a sample with both the SNP and the insertion at that location, and that one (surprisingly) did count the insertions in AD. Probably a different issue (due in part, I'm guessing, to the SNP and indel callers being different processes), but the 0/1 call for the SNP and 1/1 call for the insertion appear to be in conflict given it's a single position:
    6 110053824 . G T 2995.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.852;DP=250;Dels=0.02;FS=3.677;HaplotypeScore=221.5300;MLEAC=1;MLEAF=0.500;MQ=55.11;MQ0=1;MQRankSum=-1.532;QD=11.98;ReadPosRankSum=-2.522 GT:AD:DP:GQ:PL 0/1:125,121:246:99:3024,0,3132
    6 110053824 rs150311668 G GT 5077.73 . AC=2;AF=1.00;AN=2;BaseQRankSum=-3.673;DB;DP=250;FS=6.039;HaplotypeScore=789.8322;MLEAC=2;MLEAF=1.00;MQ=55.11;MQ0=0;MQRankSum=0.347;QD=20.31;RPA=13,14;RU=T;ReadPosRankSum=-0.080;STR GT:AD:DP:GQ:PL 1/1:35,187:249:92:5115,92,0

    all the best,

    Post edited by celzinga on
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Can you try with 2.4 and tell us if the problem persists?

  • This post is rather old, but I was wondering if anyone was able to solve this issue. I am testing out GATK version 2.3-9 and I'm seeing a number of variants with AD=0,0, despite having very high variant qualities and coverage. While most are indels, some are single base changes. Any help would be appreciated!

  • SheilaSheila Broad InstituteMember, Broadie, Moderator



    We do not support version 2.3-9. Please upgrade to the latest version and see if the problem persists.


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