zilong-li / vcfppr Goto Github PK

Hi Zilong-Li,

Thank you for your software. I found it from your reply here.

I am currently trying to use vcfcomp to test concordance between some imputed genotypes and their original genotypes using the following script:
library(vcfppR)
res <- vcfcomp(test = "x.vcf.gz", truth = "y.vcf.gz", region="z|z", af="af.tsv", stats = "r2")
str(res)
write.table(res, file = "concordance", sep = "\t", col.names = T, row.names = T, quote = FALSE)

I used vcftools --freq to output the allele frequency for af.tsv.

However, this returns a dataframe fulls of NAs:

str(res)
List of 2
$ samples: chr [1:25] "/fastdata/bop21kgl/RawData/LIMS26076p5/Clean_aligned/418-2054_221014_L003__all_mapped_rehead.bam" "/fastdata/bop21$
$ r2 : logi [1, 1:17] NA NA NA NA NA NA ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:17] "(0,1e-05]" "(1e-05,2e-05]" "(2e-05,5e-05]" "(5e-05,0.0001]" ...
write.table(res, file = "concordance", sep = "\t", col.names = T, row.names = T, quote = FALSE)

proc.time()
user system elapsed
190.199 5.955 196.606

Do you have a suggestion of where this is going wrong?