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low DP value after using GATK 4.0.12 Haplotypecaller
Dear GATK team,
I am using GATK 4.0.12 Haplotypecaller for calling the variants from the data of Targeted Amplicon sequencing.
however, the DP value of the .vcf is much lower than the value in BAM file viewing with IGV.
May i ask you how to figure out this issue?