Question: Merging vcf files ?
gravatar for Picasa
2.9 years ago by
Picasa390 wrote:

I have 8 individuals from whom I run variant analysis (with GATK). So I have now 8 .vcf files.

These 8 individuals can be splitted into 2 groups and that's what I wanted to know.

Is there a way to merge the 8 .vcf files and to perform a kind of GWAS analysis to discriminate my samples ? Do you have any recommendation for a method ?


vcf • 1.6k views
ADD COMMENTlink modified 3 months ago by jaybee10 • written 2.9 years ago by Picasa390

If you can clarify more. Do you perform non somatic variant call or variant call having both somatic and germline? Check this thread

Vcftool is there do so such.

Just check this post carefully and see before performing the merge.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by ivivek_ngs4.8k


How is it important between non somatic and with somatic ??

ADD REPLYlink written 2.9 years ago by Picasa390

It depends on your biological reasoning about what you are actually interested in, if you are trying to find mutations that is driving the disease specfic to your patients (exclusive or common) against control data of a family member who does not have the disease then it might help you in defining the mutations that are germline/somatic/ de novo. Then you can always associate them with any standard annotation softwares like ANNOVAR, SNPeff or VEP.

ADD REPLYlink written 2.9 years ago by ivivek_ngs4.8k

vcftools has vcc-merge module. It might help you through with the merging multiple vcf files.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by morovatunc400
gravatar for jaybee
3 months ago by
South Korea
jaybee10 wrote:

You can try /PATH/to/bcftools merge Home/data/*vcf.gz -Oz -o Merged.vcf.gz

[considering that your files A.vcf.gz , B.vcf.gz and so on are in the Home directory, under the folder data]

[If your bcftools is installed in the usr/bin directory then simply use:

/usr/bin/bcftools merge Home/data/*vcf.gz -Oz -o Merged.vcf.gz

This should work fine!

ADD COMMENTlink written 3 months ago by jaybee10
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