Discrepancy between VCF and BAM file.

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3 months ago

franklin • 0

enter image description here During 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 • 404 views

ADD COMMENT • link updated 3 months ago by Ram 44k • written 3 months ago by franklin • 0

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Depth. Quality, clipping., Sam flags ...

ADD REPLY • link 3 months ago by Pierre Lindenbaum 164k

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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.

ADD REPLY • link 3 months ago by microfuge ★ 1.9k

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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.

ADD REPLY • link 3 months ago by Ram 44k

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