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inconsistent result between .bam file and vcf file

Hi, @GATK.team,

I was using GATK 3.8.1 HaplotypeCaller for variants calling in PCR-targeted-region sequencing samples after mapping.
however, the results of the variants called in .vcf were inconsistent with the .bam showing in IGV.
and one SNP variant is frequently found in several .vcf of several samples, but in each .bam of the samples, the actual ref:alt=100% : 0%, which means it shouldn't be SNP variants.

so for this issue, may i ask you what the problem it is and what should i do?

Answers

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