To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

what is defined as a candidate region in haplotypecaller?

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.

Sign In or Register to comment.