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LucaB

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  • HaplotypeCaller and SoftClipped bases

    Hi,When analyzing a WES sample for variant calling, we observed a heterozygous SNV with an allele depth (AD) of 36,28 in the gVCF/VCF. However, upon inspection in IGV, only 3 alternative bases are ...

  • 0 AD/DP for called variant in HaplotypeCaller

    Hi, I am using GATK v.4.5.0.0. and calling variants with HaplotypeCaller. While investigating the minimum variant allele frequency called by HaplotypeCaller, I noticed that some variants are called...