alachins
commented
1 year ago 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
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!
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-- Nikolaos Alachiotis
Harper75
idaios
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!