Depth in multisample calling

mehar

Hi,

I have used GATK for multi sample SNP calling, the total depth DP at the variant site does not seem to be the same when the individual depths are summed up for few of the variants. For example, for the below shown variant site, DP=24 in the INFO column and from the FORMAT column depth= 3+3+8+2=16. chr1 3015369 . C A 39.22 AC=4;AF=1.00;AN=4;DP=24;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=4;MLEAF=1.00;MQ=6.96;MQ0=21;QD=2.45;SB=-2.321e+01 GT:AD:DP:GQ:PL ./. 1/1:3,3:6:6:48,6,0 1/1:8,2:10:3:25,3,0

Could someone give an explanation for differences in depths?

Geraldine_VdAuwera

Please read this article:

http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_annotator_DepthPerAlleleBySample.html