ksiewert
commented
3 years ago Hi Benoit,
Great question (and smart to check this)! At low allele frequencies some scans for balancing selection can be prone to false positives. I think you'll find the discussion of the -m parameter in this section of the BetaScan wikihttps://github.com/ksiewert/BetaScan/wiki/Basic-Usage#explanation-of-parameters relevant. In humans we find setting the -m parameter to .15 to be sufficient to remove false positives. If zebrafish have a higher effective population size than humans, you may be able to go a bit lower than this. Hope this helps and let me know if you have any more questions.
Best, Katie
From: benoitnabholz @.> Sent: Friday, April 2, 2021 10:09 AM To: ksiewert/BetaScan @.> Cc: Subscribed @.***> Subject: [ksiewert/BetaScan] Unexpected results (#9)
Dear Katherine,
We recently used Betascan2 on the datasets generated by Singhal et al. 2015 (https://science.sciencemag.org/content/350/6263/928.abstracthttps://urldefense.proofpoint.com/v2/url?u=https-3A__science.sciencemag.org_content_350_6263_928.abstract&d=DwMCaQ&c=WO-RGvefibhHBZq3fL85hQ&r=RCZkW2_0szgFcbgrJQDVb0JJbsAhoWepiDItwyb9mwg&m=WdutRlHsurzebXIFWhaQX3_2wCr5F-9yFTMZrQcpG8k&s=X5kmGGRUG82dFtOUT4Qgi0j7CI-ZV-c8S84oRnDQFFI&e=). This dataset is composed of 19 Zebra finch individuals sequenced at a coverage >10X.
When we applied Betascan2 (both the folded and unfolded version), I was surprised to see that the SNP with the highest Beta* statistics had, on average, a frequency that were lower than the rest of the genome (typically a frequence = 3% vs 5%).
Do you have any idea of what is going one? Do you have any advice on what should we check to see if the program is running correctly?
Thank-you for your help, Benoit Nabholz
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benoitnabholz
Dear Katherine,
We recently used Betascan2 on the datasets generated by Singhal et al. 2015 (https://science.sciencemag.org/content/350/6263/928.abstract). This dataset is composed of 19 Zebra finch individuals sequenced at a coverage >10X.
When we applied Betascan2 (both the folded and unfolded version), I was surprised to see that the SNP with the highest Beta* statistics had, on average, a frequency that were lower than the rest of the genome (typically a frequence = 3% vs 5%).
Do you have any idea of what is going one? Do you have any advice on what should we check to see if the program is running correctly?
Thank-you for your help, Benoit Nabholz