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HaplotypeCaller and Reduced Reads
I noticed that the statement "The interaction between the HaplotypeCaller and ReducedReads is still being worked out" is not in Guidebook of the lasted version (2.5.2) now. Does it mean that HaplotypeCaller now works well with Reduced BAMs and has the same accuracy as calls from un reduced BAMs, like UnifiedGenotyper? If this is true, it will certainly reduce the processing time of calling variants. Thanks in advance.