Merging vcf files ?

Question

[Picasa]

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 ?

Thanks.

[ivivek_ngs]

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.

[Picasa]

Hi,

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

[ivivek_ngs]

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.

[morovatunc]

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

Answer 1

[jaybee]

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!

Answer 2

[fotaye7734]

Softaken Merger VCF is a highly efficient and reliable tool that merges multiple VCF files into one combined VCF file. This innovative utility offers a cost-effective and reliable option to merge vCard Contacts and other mail items into a single file.