Tobias Rausch

Hi Sarah, These are the standard mappability maps of delly's cnv module: [https://github.com/dellytools/delly?tab=readme-ov-file#read-depth-profiles-and-copy-number-variant-calling](https://github.com/dellytools/delly?tab=readme-ov-file#read-depth-profiles-and-copy-number-variant-calling) Best, Tobias

Indigo just runs tracy in the backend: `tracy decompose -v -r MBL2.gene.slice.fa -q 50 -u 750 -p 0.3 MF-102_MBL2.ab1`

I am afraid we don't have a better solution for the annotation with RS identifiers with a gene sequence as input.

Delly only evaluates paired-end mappings. So as long as you used an appropriate mapper for WGBS data it should work but I haven't tested this. Delly is not aware of...

Hi Nicola, HOMLEN and INSLEN are available for all SV types because these INFO fields encode the length of any micro-homology or micro-insertion found at the SV breakpoint (for all...

Alignments and delly have to use the same reference genome. This caused many problems in the past and that's why delly is very strict and requires the same reference genome.

-k sets the initial k-mer length. With default options, dicey enumerates the neighborhood of this k-mer at edit distance 1 and then searches these k-mers in the genome for all...

Hi Brice, For primer searches we developed `dicey search` and the web application [silica](https://www.gear-genomics.com/silica/) because this subcommand includes Tm calculations, primer hits and amplicon predictions and this tool accepts a...

Sure, I write that down as an enhancement for the future. Thanks for the suggestion!