Recently we got a Illumina custom amplicon prepared for our project. The illumina provided us score as regards to their sequence coverage where anything with greater 60% being good. We got the data running around 24 samples per flow cell. The coverage is highly variable plus the variant calls looks suspicious with many same variant calls called in most of the samples.
I need suggestions if this data can be cleaned up anyhow or is it in this condition still usable.
Thanks in advance!