what is defined as a candidate region in haplotypecaller?

drramkidrramki Posts: 3Member

I learn that HaplotypeCaller looks for candidate regions and builds a denovo assembly. So how is this region defined? How big is the region?

Recently we found a six base pair insertion in an interesting gene using HaplotypeCaller which UnifiedGenotyper missed. We sanger sequenced it and found it to be true. Happy!!! But when I tried to write a bam file with bamout option using a 1MB flanking window and the alignment looked totally new and the variant disappeared. In fact there were no reads covering that position in the new assembly.

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