Tobias Rausch

Hi, The optional BED file of target regions will not affect the whole-genome statistics. For the [Alfred web app](https://gear.embl.de/alfred/) you will get the same statistics in the "Summary stats" tab...

For genotyping your candidate somatic SVs in a set of control genomes you need to use the output file from the pairwise somatic filtering, `${delly2_dir}/${tumor_id}.pre.bcf`: `delly2 call -g ${GRCh38} -x...

(1) For a single-sample you cannot apply delly filter as written in the README. (2) Adding samples to an already existing genotyped BCF file is indeed tricky. We don't have...

(1) The germline filter only helps for specificity not sensitivity. (2) If all the samples are available you can run the standard germline workflow. Please see the [README](https://github.com/dellytools/delly#germline-sv-calling).

Hi James, Delly doesn't directly support S3 buckets but you can mount an S3 bucket as a file system using [goofys](https://github.com/kahing/goofys). I assume the performance is similar but I haven't...

I haven't benchmarked on AWS so I can't comment on the billing aspects. For your questions: (1) Should be fine. (2) I don't know. (3) Instead of mounting an S3...

Thanks, would be great if you can post your experiences here afterwards.

Looks like some problem with the sample sheet. Can you please do: `dos2unix NK_HYNK_sample.tsv` Afterwards check that the columns are okay, e.g., `cut -f 1 NK_HYNK_sample.tsv` and `cut -f 2...

Maybe the sample names do not match the input BCF file? Can you try: `bcftools view "$SV_outDir"DELLY/012.bcf | grep -m 1 "^#CHROM"`

The BED file is not a mandatory option. If it is empty you shouldn't specify it on the command-line.