Tobias Rausch

You need to contact the sequencing provider how they prepared the libraries. This doesn't seem like a standard protocol for whole genome sequencing when many of your samples have an...

Difficult to say, paired-end mapping will certainly not work.

The web applications are available at [www.gear-genomics.com](https://www.gear-genomics.com/) and thus, you do not need to install these locally. The backend command-line program [tracy](https://github.com/gear-genomics/tracy) is available via bioconda, as a static binary...

Indigo runs [tracy](https://github.com/gear-genomics/tracy) in the backend. `tracy decompose ...`

For the `consensus` subcommand this would not work because reads need to overlap the input position. `alfred` computes a classical multiple sequence alignment around that input position.

Usually we prefer to parallelize by patient, i.e., run multiple jobs with matched tumor-normal samples in the cluster. If you are not interested in sub-clonal mutations, you can also increase...

We usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output for BND events linking the additional sequence to the regular...

Most short-read SV callers do not attempt SV breakpoint assembly and that is, what delly stores in INFO/CONSENSUS. INFO/CONSBP indicates the SV breakpoint position on that consensus sequence. For long-reads,...

You need to install the boost libraries, e.g., for ubuntu: `apt install libboost-date-time-dev libboost-program-options-dev libboost-system-dev libboost-filesystem-dev libboost-iostreams-dev`

Wally uses the BAM index to parse through all reads of a given region. So the default order is coordinate-sorted and any other order would require storing the reads in...