Which vcf to get manhattan plots?

[Harper75]

Hello,

I am using RAISD to identify selective sweeps in three different populations of an insect and I have been having trouble to get manhattan plots from my analyses. I am wondering if is related to the type (or size) of the vcf used.

When I use a complete vcf (all the individuals from the three populations together) with no missing data, leaving only biallelic sites, non binned (or pruned) and with no MAF filtering, I will not get the plot. If I split that vcf in the three different populations and analyse each separately, I will not get plots either.

However, if I filter for maf (0.05), do the binning, remove missing data, leave only biallelic sites and split the vcf in the three different populations, I will get plots for each population. Nevertheless, I wont get a plot of this binned vcf if I do not do the split and leave the individuals from all the populations together.

Although I want to look for differences in selective sweeps between populations, the fact that I get plots from some vcf's and not others makes me wonder which is the vcf that should be used for the analyses? Could you please help me with this?

Thanks for your help!

[alachins]

Hi, The type and size of VCF is/should not be related to the Manhattan plot generation. Do you get text reports for all of the run configurations that you tried, even those that did not create a Manhattan plot? Nikos

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On Fri, Jun 2, 2023 at 11:59 AM Harper75 ***@***.***> wrote: Hello, I am using RAISD to identify selective sweeps in three different populations of an insect and I have been having trouble to get manhattan plots from my analyses. I am wondering if is related to the type (or size) of the vcf used. When I use a complete vcf (all the individuals from the three populations together) with no missing data, leaving only biallelic sites, non binned (or pruned) and with no MAF filtering, I will not get the plot. If I split that vcf in the three different populations and analyse each separately, I will not get plots either. However, if I filter for maf (0.05), do the binning, remove missing data, leave only biallelic sites and split the vcf in the three different populations, I will get plots for each population. Nevertheless, I wont get a plot of this binned vcf if I do not do the split and leave the individuals from all the populations together. Although I want to look for differences in selective sweeps between populations, the fact that I get plots from some vcf's and not others makes me wonder which is the vcf that should be used for the analyses? Could you please help me with this? Thanks for your help! — Reply to this email directly, view it on GitHub <#43>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCR3HUAVQIPD7WV74IDXJG2PJANCNFSM6AAAAAAYYC7S7A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Nikolaos Alachiotis

[Harper75]

Thanks for your quick reply.

Yes I do get a report for each chromosome either with or without plot.

Thanks again

[alachins]

Can you send me the reports from a run that did not generate a manhattan plot? Nikos

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On Fri, Jun 2, 2023, 16:08 Harper75 ***@***.***> wrote: Thanks for your quick reply. Yes I do get a report for each chromosome either with or without plot. Thanks again — Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCQP4WLVYGY6BHO7RJDXJHXU5ANCNFSM6AAAAAAYYC7S7A> . You are receiving this because you commented.Message ID: ***@***.***>

[Harper75]

Here they are!

Thank you very much for all your help.
report_raisd.zip

[alachins]

One of the sets does not contain any SNPs. This might be the reason that it didn' t generate the plot.
You can use the following ReportList and script to get the Manhattan plot.

rscript-manhattan.txt

RAiSD_ReportList.pop1.txt

[alachins]

You can call it like this: Rscript rscript-manhattan.txt pop1 0.995
and you get this (less sets in this example):
RAiSD_ManhattanPlot.pop1.pdf

[Harper75]

Great, thanks a lot for your help!

[idaios]

I also think that this might be the reason pavlos

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On Mon, Jun 12, 2023 at 11:24 AM alachins ***@***.***> wrote: One of the sets does not contain any SNPs. This might be the reason that it didn' t generate the plot. You can use the following ReportList and script to get the Manhattan plot. rscript-manhattan.txt <https://github.com/alachins/raisd/files/11720043/rscript-manhattan.txt> RAiSD_ReportList.pop1.txt <https://github.com/alachins/raisd/files/11720047/RAiSD_ReportList.pop1.txt> — Reply to this email directly, view it on GitHub <#43 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAE553VVZKB73UE764LKKFTXK3G3ZANCNFSM6AAAAAAYYC7S7A> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Pavlos Pavlidis, PhD