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HaplotypeCaller calling as heterozygotes incorrectly

I am finding that HaplotypeCaller is calling heterozygotes when there is no evidence when you look in IGV. Is this still a known problem?

I am using version 2.8-1-g932cd3a. Attached are two screen shots in IGV where a heterozygotes is wrongly called:

Variant callers 7.jpg
750 x 600 - 86K
Variant callers 8.jpg
750 x 600 - 81K

Answers

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