Entering edit mode
8.6 years ago
aga.lipinska
•
0
Dear all,
I have been using PopGenome with VCF files to get some neutrality statistics for RAD-Seq data. I used mpileup and bcftools to get the variant calls and have individual VCF files per chromosome with genotype data for 3 populations and 1 outgroup. Everything seems to work, but I am getting these strange values for Tajima's D above 5 and more. These values only appear when I use the option set.populations:
get.neutrality(data)[[1]] #(population 1)
Tajima.D n.segregating.sites Rozas.R_2 Fu.Li.F Fu.Li.D Fu.F_S Fay.Wu.H Zeng.E Strobeck.S
test 9.555944 183 NA 5.185575 1.276137 NA 4.054317 -6.170585 NA
If I treat my samples as one populations I get:
get.neutrality(data)[[1]] #(all populations)
Tajima.D n.segregating.sites Rozas.R_2 Fu.Li.F Fu.Li.D Fu.F_S Fay.Wu.H Zeng.E Strobeck.S
test 1.353448 1018 NA 1.400123 0.999412 NA NaN NaN NA
Below are the commands I use:
data <- readData(path="./vcf", format="VCF", include.unknown=TRUE, gffpath="./gff")
data <- set.populations(data, list(c("ind1", "ind2"..), c("ind3", "ind4"..), c("ind5", "ind6"..), c("ind7", "ind8"..)), diploid=TRUE)
data <- set.outgroup(data, c("ind1", "ind2"..), diploid=TRUE)
data <- neutrality.stats(data)
get.neutrality(data)[[1]]
What could be the problem? If anyone has any suggestions, I would be very grateful!