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VariantAnnotator doesn't annotate Coverage at every call

apolyakapolyak State College, PA, USAMember

Some calls I don't see allele depth (AD), for some I don't see depth (DP), and for some I see neither. Are there scenarios where GATK cannot annotate these?

Answers

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin

    @apolyak
    Hi,

    Can you please tell us the exact command you ran and the version of GATK you are using?

    Thanks,
    Sheila

  • apolyakapolyak State College, PA, USAMember
    edited January 2016

    I'm using GATK 3.3, and was hoping to not upgrade as that would take a lot of time to rerun the entire pipeline (unless doing so wouldn't be required).

    This is the command:

    java -Xmx10g -jar $GATKDIR/GenomeAnalysisTK.jar \
     -R $REF \
     -T VariantAnnotator \
     -nt 6 \
     -I sample1.bam \
     -I sample2.bam \
     -I sample3.bam \
     -I sample4.bam \
     -I sample5.bam \
     -I sample6.bam \
     -I sample7.bam \
     -I sample8.bam \
     -A DepthPerAlleleBySample \
     -A Coverage \
     -V all_samples.vcf \
     -L all_samples_annotated.vcf \
     -o PSU001_annotated.vcf
    

    And it outputs a file with some calls such as:

    chr1    15118   .       A       G       5277.48 VQSRTrancheSNP99.90to100.00     AB=0.256231;ABP=520.702;AC=10;AF=0.385;AN=26;AO=269;BVAR;BaseQRankSum=5.29;CIGAR=1X;DP=3130;DPB=1321;DPRA=0.776693;EPP=196.949;EPPR=1014.46;FS=3.239;GQ_MEAN=374.85;GQ_STDDEV=354.90;GTI=1;InbreedingCoeff=-0.6774;LEN=1;MEANALT=1.91667;MLEAC=11;MLEAF=0.423;MQ=26.67;MQ0=0;MQM=10.7063;MQMR=11.4812;MQRankSum=0.171;NCC=0;NS=13;NUMALT=1;ODDS=6.5679;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=8632;QD=4.76;QR=26423;RO=1037;RPP=519.716;RPPR=1969.19;RUN=1;ReadPosRankSum=1.14;SAF=51;SAP=228.141;SAR=218;SOR=0.396;SRF=147;SRP=1159;SRR=890;TYPE=snp;VQSLOD=-7.897e+00;culprit=MQ;dataset=Intersection;technology.illumina=1    GT:AD:DP:GQ:PL:TP
    0|1:216,32:.:99:229,0,3460:120  0/1:118,129:.:99:1286,0,906     0/1:214,35:.:82:82,0,2344       0/1:215,30:.:97:97,0,2678       0/0:249,0:86:99:0,120,1800      1|0:146,67:.:99:591,0,1221:120  0|0:245,2:66:99:0,120,1800:120  0/1:201,38:.:99:106,0,1954      0/1:96,103:.:99:1166,0,844      0/0:209,37:99:0:0,0,2313        0/1:185,60:.:99:1026,0,2202     0/1:197,48:.:99:300,0,2163      0/1:161,77:.:99:452,0,1539
    

    In this case, it's giving allele depth, but not depth. Shouldn't it also give a depth? Why is there a "." here instead of a depth?

    Post edited by apolyak on
  • Geraldine_VdAuweraGeraldine_VdAuwera admin Cambridge, MAMember, Administrator, Broadie admin

    I think this was a bug where specifying the Coverage annotation actually disabled it. Can you try running without specifying it?

  • apolyakapolyak State College, PA, USAMember

    Actually, one problem is that some calls have the depth annotation, and others have "." and others have no genotype DP annotation at all.

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