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Order of reporting sites by GenotypeGVCFS
When I genotype a large and diverse cohort I often see an error about too many alleles at one position, which is fine. What puzzles me is why the sites in question are not reported in order, e.g. here position 102k is highlighted after 501k:
INFO 20:56:15,037 ProgressMeter - 0101:9012801 0.0 30.0 s 50.1 w 2.4% 21.2 m 20.7 m
WARN 20:56:26,448 GenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location 0101:5019574
WARN 20:56:43,879 GenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location 0101:1023160
As far as I can tell the sites are ordered in the gVCFs. Is this an unimportant idiosyncrasy of the Progress Meter output, or does it point to a problem with my input files?