running Delly by chromosome?

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Heidi Yang

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Jul 18, 2023, 5:43:51 PM7/18/23

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Hi,

I have 59 15x WGS samples I'd like to run Delly on and the ref genome size is ~850 Mb. I was considering breaking the runs up by chr to improve runtime, but I wouldn't be able to detect interchromosomal translocations. Or should I run all samples together and give it more cores and memory? Alternatively, should I just make individual bash scripts for each sample and run those in parallel? Thanks in advance!

Best,

Heidi

Tobias Rausch

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Jul 19, 2023, 4:14:10 AM7/19/23

to Heidi Yang, delly-users

Hi Heidi,

Depends whether you are interested in somatic or germline SVs. I have put some exemplary workflows on Github: https://github.com/dellytools/delly#somatic-sv-calling

Best, Tobias

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