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.
Could you please explain how to run DELLY on Galaxy?
The job failed so what am I doing wrong?
Give a link to the genome file used for DELLY input?
A genotyping file and its explanation will be appreciated.