Question: use of Selscan to analyse candidate region?

[miletj]

Hello,

Is it possible to use Selscan to calculate iHs and nSL on a candidate region?
Who can do more can do less, so I suppose the answer is yes. Does this pose any technical problems?

I would like to apply it to HLA region which have been reimputed. I have already the iHS and nL for the same population on the whole genome.

Thank very much.

Regards.

Jacqueline

[szpiech]

Hi Jacqueline, Unfortunately, you can't easily re-scan a specific genomic region with selscan, and there are some technical reasons why I might not suggest doing it anyway. However, you can re-scan the entire chromosome that your HLA genes are on, and then use that along with the previous results for a new normalization computation. Also, if you're not using it already, selscan 2.1 is dramatically faster than previous versions. Zachary

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On Fri, Jul 4, 2025 at 6:59 AM miletj ***@***.***> wrote: *miletj* created an issue (szpiech/selscan#146) <#146> Hello, Is it possible to use Selscan to calculate iHs and nSL on a candidate region? Who can do more can do less, so I suppose the answer is yes. Does this pose any technical problems? I would like to apply it to HLA region which have been reimputed. I have already the iHS and nL for the same population on the whole genome. Thank very much. Regards. Jacqueline — Reply to this email directly, view it on GitHub <#146>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABAKRQUKBWM5QVNACFGZFKL3GZNA7AVCNFSM6AAAAACAZELOX6VHI2DSMVQWIX3LMV43ASLTON2WKOZTGIYDEMRWGE4DMMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[miletj]

Thank you very much for your answer.
All the best,