Hi, I am trying to use the vcftools to get some summary statistics about my VCF file. The file is properly sorted and indexed. But, When I was using the following functions:
The tool did not give out any results but a blank sheet. Here is the message from the screen printout about TajimaD, but the heterozygosity calculation displayed the similar message. My vcf file is not annotated. Do you think thats why it showed "CONTIG declaration found without ID: /A" ? Or it is because of something else, and what else could cause this? Thank you very much !
Code:
zcat my.sorted.vcf.gz | vcftools --vcf - --het --out het zcat my.sorted.vcf.gz | vcftools --vcf - --TajimaD 20 --out TajimaD
Code:
VCFtools - v0.1.12
(C) Adam Auton and Anthony Marcketta 2009
Parameters as interpreted:
--vcf [stdin]
--out TajimaD.out
--TajimaD 20
CONTIG declaration found without ID: /A
After filtering, kept 81 out of 81 Individuals
Outputting Tajima's D Statistic...
TajimaD: Only using fully diploid sites.
After filtering, kept 2592 out of a possible 2592 Sites
Run Time = 1.00 seconds