ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexity, such as the entire RepBase database. It is easy to install and use with command lines.
Learning from the step-by-step guide on using ERVcaller, I'm curious about the filter criteria in step03. What's the difference between 'variable 2' and 'variable 5'？And for the data with average read depth over 45, should I adjust the filter criteria to some extent?
Besides, expecting your advice for how to set the -S and -n parameter in calling step, if the read length is 100bp.~
Sorry for the confusion, I think variable 2 is to filter by the aggregated DPIs across samples and variable 5 is to filter by the minimum DPIs per site per sample. And I think the variable for the per sample one will be more important.
xunchen85
commented
1 month ago
Hello Dr.Chen,
Learning from the step-by-step guide on using ERVcaller, I'm curious about the filter criteria in step03. What's the difference between 'variable 2' and 'variable 5'？And for the data with average read depth over 45, should I adjust the filter criteria to some extent?
Besides, expecting your advice for how to set the -S and -n parameter in calling step, if the read length is 100bp.~
Thank you so much!
Yaaoo