Discrepancy between VCF and BAM file.
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franklin •
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GATK haplotypecaller has an
--bam-outoutoption to generate a bam with locally realigned reads ( https://gatk.broadinstitute.org/hc/en-us/articles/360037225632-HaplotypeCaller ) for debugging. Generating a bam in this case could be of use to determine why the call was made.Please do not delete posts that have received feedback. Instead, interact with the people that have invested effort into helping you, and work towards providing closure to your post.