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GATK somatic CNV pipeline NaNs
Dear GATK Team,
I ran the GATK somatic CNV calling pipeline on Terra (v1.3.1 for the PoN and 1.3.0 for the somatic pair workflow) on unpaired canine tumor WGS data. I noticed that I am seeing runs of NaNs in portions of the ModelSegmentsTumor output (in the MINOR_ALLELE_FRACTION columns), corresponding to locations where NUM_POINTS_ALLELE_FRACTION is zero. Is this something that is expected, or a sign that there is a problem?
chr26 29292001 29467000 168 0 1.494626 1.511347 1.528258 NaN NaN NaN chr26 29467001 29829000 325 0 0.802825 0.814096 0.828611 NaN NaN NaN chr26 29829001 30150000 231 0 1.690182 1.700493 1.721356 NaN NaN NaN chr26 30152001 30391000 188 0 0.830539 0.850131 0.868545 NaN NaN NaN
In this run, the list of chromosomes passed in for the intervals argument was not sorted numerically, so the tool plotted the chromosomes out of order. Would this cause any problems if the PoN was not in the same order?
Thank you for your help!