why GATK and BCFTOOLS output different number of DP

Question

[bxia]

I am using Miseq to check the SNPs

GATK output the AD 702, but BCFtools are 14672. Total reads are about 15000+

I used fixed primers to amplify a specific region on the genome.

Thanks

[finswimmer]

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

[bxia]

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