I am using GATK to call the variants that were ran on MiSeq platform, following the general pipeline without VQSR and dedup steps.
However, it seems hat the DP and AD values appeared in VCF file are totally different against IGV.
I read the thread that posted in GATK forum, which considered that the HC will remove some reads to do the realign for better variants calling.
However, this will lead to reduced AD and DP values, and I can not take these values seriously for QC metrics, for example, we might need to filter those variants that with DP<30.
Although I can add the -dcov FILTER in pipeline, there are not directly values for AD and DP in VCF file.
Is there anyone know how to obtain the "match-ble" values in GATK?
ps, I know it can be extracted from bam by samtools and bcftools, just want to know if can be done in GATK directly.