We used multiplex PCR to enrich the target regions, and then get them sequenced on HiSeq platform.
For germline variants, it will be ideally that the ratio for ref allele against alt is around 0.5 for heterozygous variants.
However, in our data, we find that sometimes, this ratio is less than 0.1 according to GATK calling result.
I am wondering why this could be happen for germline variants?
And the most confusing thing is that we find calling results differently but slightly difference for this ratio, etc., 0.06 for homozygous but 0.07 for heterozygous.
It will be great if you can give me some suggestions.