Tobias Rausch

(1) Better to leave the marked duplicates in the BAM. (2) Do it pairwise tumor-normal and not altogether.

I think what Lumpy encodes as INFO/STRANDS is the same as Delly's INFO/CT. As far as I know both notations are not in the VCF specification but indeed useful.

Thanks. Compared to the original publication, Delly has actually changed significantly. The latest changes are mainly related to long read SV calling. I'm afraid that at the moment the only...

This seems to be a VCF file after snpEff processing. Can you please check the original output VCF of delly if the ALT column contains symbolic values like or the...

I see. Thanks for letting me know. I will try to fix this in the next version, for an insertion there should always be an ALT sequence. For the time...

Unfortunately different SV tools use different nomenclatures but I found [this Figure](https://www.nature.com/articles/s41596-019-0234-7/figures/12) quite helpful to clarify some misunderstandings. Essentially these 4 intra-chromosomal connection types can also occur for inter-chromosomal connections...

The sub-telomeric regions are very repetitive so these SVs are likely not in high-confidence regions of the genome. It could also be that both alleles are non-reference and thus you...

Probably easier to output the BCF: `delly call -o ${SAMPLE_ID}.bcf -g ${FASTA} ${INPUT_DIR}/${SAMPLE_ID}.rmdup1.bam`

Sure, once the run is complete there should be a BCF output file for each SV type.

Probably Ns in the reference or very low mappability.