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arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
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Use of lumpy in haploid organisms #368

Open pabloangulo7 opened 2 years ago

pabloangulo7 commented 2 years ago

Hello,

I would like to use this tool in an haploid organism. It would be possible? If so, what parameters should I modify?

Thanks

Pablo

ryanlayer commented 2 years ago

What is the coverage?

On Tue, Oct 19, 2021 at 11:02 AM pabloangulo7 @.***> wrote:

Hello,

I would like to use this tool in an haploid organism. It would be possible? If so, what parameters should I modify?

Thanks

Pablo

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pabloangulo7 commented 2 years ago

I have 25 samples. The coverage are (58X,43X,66X,56X,55X,20X,30X,26X,54X,51X,69X,47X,52X,22X,55X,96X,65X,40X,23X,40X,43X,49X,9X,43X,54X) and that would be without removing duplicates, unmapped or secondary alignments.

ryanlayer commented 2 years ago

Oh that more than I expected. What species?

There should be no issue given those coverages. Try using smoove. It makes the whole process much easier.

https://github.com/brentp/smoove

On Oct 20, 2021, at 4:43 AM, pabloangulo7 @.***> wrote:

 I have 25 samples. The coverage are (58X,43X,66X,56X,55X,20X,30X,26X,54X,51X,69X,47X,52X,22X,55X,96X,65X,40X,23X,40X,43X,49X,9X,43X,54X) and that would be without removing duplicates, unmapped or secondary alignments.

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