Intervals specified using vcf files are off by 1

raylimraylim Posts: 1Member

I tried specifying intervals using a vcf file to HaplotypeCaller and I'm not getting the appropriate hits, because it appears that GATK is interpreting the vcf file as 0-based.

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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,163Administrator, GATK Developer admin

    That shouldn't happen. Can you please post what was your command-line, positions of interest and results?

    Geraldine Van der Auwera, PhD

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