Popgenome nvalid sites

0

Hi all,

I would like to use the r program popgenome to calculate some neutrality stats. However, everytime that I read the data I have 0 or NaN valid sites.

For example, if I read all chromosome 1 like this:

GENOME.class_all <- readVCF("File.vcf.gz", numcols=100000, tid="Chr01", frompos=1, topos=159207788, include.unknown=T)

I have this:

get.sum.data(GENOME.class_all)

                           n.sites     n.biallelic.sites n.gaps n.unknowns n.valid.sites
1 - 159207788 159207788             85427          0                  0                0
                       n.polyallelic.sites trans.transv.ratio
1 - 159207788                        0                    NaN

Playing with the numcols, frompos, and topos parameters sometimes I have n.valid.sites 0 or NaN but apparently popgenome is not recognizing any valid site.

My vcf file was imputed with beagle5 and for Chr01 I have 91955 sites for 25 individuals, where the last SNP has the position 159207788. I am wondering if I am doing something wrong.

Best Wishes,

Eric


vcf


Popgenome

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