Use of lumpy in haploid organisms

[pabloangulo7]

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]

What is the coverage?

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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 — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#368>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAEUGUPW4I3RY56XDT6EU5LUHWQDRANCNFSM5GJUPNBQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[pabloangulo7]

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]

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

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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. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.