Hello,
In our pipeline we have a quality control step where 23 snps are called with GATK and with realtime PCR. Lately as the coverage depth increases, we start to see that TaqMan is calling a homozygous snp and the high throughput sequencing method a heterozygous snp. And this mostly in case where one allele is present below 10%.
I have difficulty to imagine cases where the allele frequency in one individual is below 10%.
Can someone help me to make sense of this?
Thanks
In our pipeline we have a quality control step where 23 snps are called with GATK and with realtime PCR. Lately as the coverage depth increases, we start to see that TaqMan is calling a homozygous snp and the high throughput sequencing method a heterozygous snp. And this mostly in case where one allele is present below 10%.
I have difficulty to imagine cases where the allele frequency in one individual is below 10%.
Can someone help me to make sense of this?
Thanks
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