Question: How to view the contents and header of a Vcf file in linux using VCFTOOLS
0
gravatar for sridevi
23 months ago by
sridevi0
sridevi0 wrote:

Hi,

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 • 3.2k views
ADD COMMENTlink modified 23 months ago by WouterDeCoster39k • written 23 months ago by sridevi0
1

If it is zipped file you can use zless

ADD REPLYlink modified 23 months ago • written 23 months ago by Medhat8.3k
2
gravatar for Pierre Lindenbaum
23 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum120k wrote:
gunzip -c ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz
ADD COMMENTlink written 23 months ago by Pierre Lindenbaum120k

Thanks u so much:) it works

ADD REPLYlink written 23 months 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 23 months ago by Pierre Lindenbaum120k
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