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No coverage information for some sites after BP RESOLUTION haplotype caller?
Dear GATK team,
We are trying to run GATK haplotype caller with BP RESOLUTION to get coverage information for each site. But it seems like some sites don't have any cov information, for example:
jcf7180012625382:4560 4560 . A G, 0.01 . MLEAC=0,0;MLEAF=NaN,NaN GT ./.
I wonder if it is because GATK is not sure about how to call this SNP because signal is too low, or there are some explanations can help me with this issue?
Thank you for the help!