I have a NGS data with coverage 10-15X, and I use the (Manta, CNVnator, Lumpy) + Svimmer + Graphtyper2 to detect SV and genotype SV. I got result which many SV site have LowPratio.
when I see the SI of original paper (Hannes P. Eggertsson et al. 2019), the criteria include:
- all genotyping models must have at least 10 unique reads
the mean coverage in my data is only 10-15X, maybe many site can't meet this criteria. So, I want to know if there are some arguments I can change the criteria?
Thanks!