How do you run Delly by chromosome? I have looked at the Delly GitHub page and I cannot find the answer. I have also looked at old questions like this Delly question but this question does not address how to run by chromosome.
I am running
delly call -t DEL -g ref.fa -o dellyOut.bcf file1.markedDup.bam file2.markedDup.bam file3.markedDup.bam file4.markedDup.bam . . . file100.markedDup.bam
For each of the structural variations I am running the options below:
-t DEL = Deletions
-t INS = Insertions
-t INV = Inversions
-t DUP = Tandem Duplications
-t TRA = Inter-chromosomal translocations
While this is okay, I would also like to run Delly by chromosome. If any of you know the list of options for Delly or where they are stated can you please post a link. I found the information about option -t by reading this Biostars question.
Thank you for your help.