How to view the contents and header of a Vcf file in linux using VCFTOOLS

Question

[sridevi]

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

[Medhat]

If it is zipped file you can use zless

Answer 1

[Pierre Lindenbaum]

gunzip -c ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

[sridevi]

Thanks u so much:) it works

[Pierre Lindenbaum]

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