Vcftools,--Diff Option

Question

[Joanne Lim]

Is there a way to compare more than two vcf files (around 50) with vcftools with the command below?

vcftools 1.vcf --diff 2.vcf

The reason that I am using this --diff option is because I am interested to get the matrix/table that shows the difference of the genotype output from my vcf files (just like the output of out.diff.sitesinfiles) So far, I am only able to compare two files.

Ideally, I would like to get a matrix that would look like this

Chr Pos Ref ALT1 ALT2 ALT3 ........ALTn

Appreciate your inputs

Thanks in advance.

Cheers,

Joanne

[Sophia]

Joanne, I just checked out the commands at vcftools documentation and did not find the option you are talking about. Are we talking about the same vcftools program?

[Sophia]

Joanne, I just checked out the commands in the documentation at vcftools.sourceforge.net/docs.html and did not find the option you are talking about. Are we talking about the same vcftools program?

Answer 1

[Sophia]

the perl modules of vcftools include some functionalities that might be of use to you:

• vcf-compare
• vcf-isec

and more...

[Joanne Lim]

Hi,I have actually tried vcf-compare and vcf-isec, vcf-compare gives me the statistics, currently i am not having any success with vcf-isec.

Ideally I would like to get a matrix that would look like this:-

Chr Pos Ref ALT1 ALT2 ALT3 ALT4 ...... ALTn

which is what the --diff options offers but it only allows me to compare 2 files.

Thanks again!