How to use DELLY with Galaxy

usegalaxy.eu support
1

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?
  3. Give a link to the genome file used for DELLY input?
  4. A genotyping file and its explanation will be appreciated.
2

Hi @Ritik_Sinha,
could you provide some information about the error? You can use the GRCh37 reference genome from NCBI in the Select genome file option. According this issue in GitHub, the *.blacklist.gz files are mappability maps.

Let me know if it works.

Regards.

3

It produced an empty file. I don’t know how to get this chr11_gl000202_random. Could you please tell me why DELLY would require this file?

No results.
BAM file chromosome chr11_gl000202_random is NOT present in your reference file /data/dnb03/galaxy_db/files/8/b/9/dataset_8b97bd82-c984-4ee1-8735-7836bf28eafb.dat

4

HI @Ritik_Sinha,
this error seems to be caused by the fact that the reference genome used in the alignment is different from the one used for running DELLY.

Regards.