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.
From the improper reads step, bwa-mem fails to read the index files - I did index both the input bam and reference genome fa files, which is why the previous step 'Chimeric and split reads' worked. Beyond that, bwa-mem does not want to work.
Hi there,
From the improper reads step, bwa-mem fails to read the index files - I did index both the input bam and reference genome fa files, which is why the previous step 'Chimeric and split reads' worked. Beyond that, bwa-mem does not want to work.
Any help would be much appreciated!