Question: How to view the contents and header of a Vcf file in linux using VCFTOOLS
gravatar for sridevi
3.0 years ago by
sridevi0 wrote:


I just installed vcftools using linux and used the command as below :

vcftools --gzvcf ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz --freq --chr 1 --out chr1_analysis

Here's what it reads:

Reading Index file.
File contains 6468094 entries and 2504 individuals.
Applying Required Filters.
After filtering, kept 2504 out of 2504 Individuals
After filtering, kept 6468094 out of a possible 6468094 Sites
Run Time = 29.00 seconds

However, I am unable to view the entries of the file. Is there any way to do it ?

Many Thanks in Advance

vcftools 1000 genomes • 7.0k views
ADD COMMENTlink modified 3.0 years ago by WouterDeCoster44k • written 3.0 years ago by sridevi0

If it is zipped file you can use zless

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by Medhat8.7k
gravatar for Pierre Lindenbaum
3.0 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:
gunzip -c ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
ADD COMMENTlink written 3.0 years ago by Pierre Lindenbaum129k

Thanks u so much:) it works

ADD REPLYlink written 3.0 years ago by sridevi0

If this answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLYlink written 3.0 years ago by Pierre Lindenbaum129k
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