Hi, I am just not sure about the concordance between GATK and Samtools mpileup.
I have one sample, and the variants called by GATK and Samtools showed 99% concordance for a total of ~3.1 million SNPs. is this number a typical one? The concordance was computed using GATK's SelectVariants module.
Thanks a lot for your advice
I have one sample, and the variants called by GATK and Samtools showed 99% concordance for a total of ~3.1 million SNPs. is this number a typical one? The concordance was computed using GATK's SelectVariants module.
Thanks a lot for your advice
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