We are using amplicon based method to enrich the target region of given SNPs. And GATK UnifiedGenotyper is applied to call the given/specific variants.
In order to test the robust the our panel, we replicate the same samples, and compared the calling results between two runs.
Over 2000 variants we are looking for, we found that some of them showed different genotypes.
We defined ABRatio as the percentage of reads stand for alt allele.
Similar depth was found between two run, however, slight ABRation change was found.
In the first run, ABRatio=0.06, wildtye genotyes 0/0 was assigned for the sample. However, 0.07 was found for this same sample in the second run. Heterozygous genotype 0/1 was assigned.
We are wondering if there is any method that can diminish this disconcordance? From calling parameter or just experiments?