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Old 03-16-2014, 06:40 PM   #1
Baoqing
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Location: Texas

Join Date: Jan 2013
Posts: 24
Default VCFtools empty results for TajimaD calculation

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:

Code:
zcat my.sorted.vcf.gz | vcftools --vcf - --het --out het
zcat my.sorted.vcf.gz | vcftools --vcf - --TajimaD 20 --out TajimaD
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:
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

Last edited by Baoqing; 03-16-2014 at 06:44 PM.
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