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GATK error by unexpected data type of SA_MAP_AF


FilterMutectCalls was shut down by a non-double value of 'NaN' for 'SA_MAP_AF'.

The error message and the corrosponding variant call by Mutect2 are below.


chr19 501743 . T C,TCTCCCGACACCACCTCCCAGGAGC . . DP=245;ECNT=2;POP_AF=5.000e-08,5.000e-08;TLOD=3.06,10.02 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/1/2:0,0,0:0.354,0.372:0,0,0:0,0,0:0,0,0:0,0,0:0,0:0,0:0.00,0.00,NaN:0.025,0.025,0.950

org.broadinstitute.hellbender.exceptions.GATKException: INFO annotation 'SA_MAP_AF' contains a non-double value 'nan'



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