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?
Can you please tell us the exact command you ran and the version of GATK you are using?
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 \
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?
I think this was a bug where specifying the Coverage annotation actually disabled it. Can you try running without specifying it?
Actually, one problem is that some calls have the depth annotation, and others have "." and others have no genotype DP annotation at all.