Discrepancy between VCF and BAM file.
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4 months ago
franklin • 0

enter image description hereDuring a WES study, I am performing variant discovery using GATK HaplotypeCaller. However, when I visualize the regions with variants shown in the VCF file on IGV, these variants do not appear in the BAM file. What could be the reason for this discrepancy?

NGS bwa haplotypecaller gatk • 419 views
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Depth. Quality, clipping., Sam flags ...

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GATK haplotypecaller has an --bam-outout option 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.

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