why GATK and BCFTOOLS output different number of DP
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17 months ago
bxia ▴ 160

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

miseq SNP • 336 views
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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

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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

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