why GATK and BCFTOOLS output different number of DP
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GATK and bcftools use different quality markers and different thresholds for them, to determine which read they take into account for variant calling and which they skip. So a difference is normal. But in your case, that's looking to different to me.
Could you please provide the commands you've used?
fin swimmer
Each of them are just default one. I am confusing because others number looks like very similar.
BCFtools gave the total number of reads almost.
But GATK were just 702