Question: Vcftools Blank Output
gravatar for mad.cichlids
6.7 years ago by
mad.cichlids120 wrote:

Hi, I am trying to use the vcftools to get some summary statistics about my VCF file. When I was using the following functions:

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 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 !

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
vcf • 3.6k views
ADD COMMENTlink written 6.7 years ago by mad.cichlids120

Did you check the TajimaD.out file? By the way, you don't need to zcat the file manually, you can use the --gzvcf option to read it directly.

ADD REPLYlink written 6.7 years ago by Giovanni M Dall'Olio27k

Thank you, Giovanni, I did check the out file. It is an empty doc with a header "CHROM BIN_START N_SNPS TajimaD"

ADD REPLYlink written 6.7 years ago by mad.cichlids120
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1143 users visited in the last hour