Attention:
The front line support team will be unavailable to answer questions until May 27th 2019 as we are celebrating Memorial Day. We will be back soon after. Thank you for your patience and we apologize for any inconvenience!

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 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 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.

Sign In or Register to comment.