Haplotype Caller Active Region
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I am getting the following output on the progress monitor of Haplotype Caller:

INFO 13:50:30,687 ProgressMeter - 17:73500593 0.00e+00 19.9 h 15250.3 w 100.0% 19.9 h 0.0 s

WARN 13:50:56,090 DiploidExactAFCalc - this tool is currently set to genotype at most 6 alternate alleles in a given context, but the context at 17:73335276 has 7 alternate alleles so only the top alleles will be used; see the --max_alternate_alleles argument

INFO 13:51:30,706 ProgressMeter - 17:73500593 0.00e+00 19.9 h 15250.3 w 100.0% 19.9 h 0.0 s

Why is it that the active region is listed as 17:73500593, yet apparently Haplotype Caller is looking at 17:73335276? It seems like ~20,000 bases away would not be considered active. What does the active region column (-f3) actually display/represent.

Thanks, -Paul Pemberton


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