How to use DELLY on Galaxy

Question

[ritiksinha005]

I am new to Bioinformatics, the DELLY documentation on GitHub is insufficient.

I am running the Galaxy Europe instance and wanna use DELLY to detect Structural Variants in the human exome paired-end data.

I have a BAM -> sortSAM -> MarkDuplicates file which I suppose would be ready for DELLY. I have mapped it to hg19.

I don't know which file to use for the Select genome file option. I have used Homo_sapiens.GRCh37.dna.primary_assembly.fa.r101.s501.blacklist.gz available at gear.embl.de/data/delly/. I don't know what effect a genotyping file will have on the calls.

1. Could you please explain how to run DELLY on Galaxy?

2. The job failed so what am I doing wrong?

   1. Give a link to the genome file used for DELLY input?

   2. A genotyping file and its explanation will be appreciated.

[lieven.sterck]

Hi ritiksinha005,

welcome.

It's not that you are not allowed to pose questions about galaxy here but you might get better/faster/more detailed feedback if you post galaxy related question on the galaxy help forum, which you can find here

[ritiksinha005]

Hi, I tried to look for it but unfortunately, there were no posts about DELLY.

[lieven.sterck]

That can very well be indeed, but you always have the option to open a new post (just as you did here)

Answer 1

[benformatics]

If you are comparing hg19 and GRCh37 physically there are minimal differences. Only the mitochondrial sequence should be different (I doubt you will be looking for SVs there). I'm not sure how GALAXY works but the chromosomes might be named differently ('chr1' vs '1', etc...) but that should error out quickly. I would guess that is the reason for the failure... your chromosome names are non-identical.

[ritiksinha005]

I have a set of 4 exome sequences for which I want to see if they contain any SVs. I have the BAM files for each (they are sorted and Duplicate marked). I am using hg19 as the reference genome.

[benformatics]

You need to check if the chromosome names match Homo_sapiens.GRCh37.dna.primary_assembly.fa.r101.s501.blacklist.gz