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.
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?
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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