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Vcftools,--Diff Option

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

vcf vcftools comparison matrix
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updated by Sophia • Sophia • written by Joanne Lim • Joanne Lim

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?

• 0 views • link
written by Sophia • 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?

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written by Sophia • Sophia

1 answer

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

  • vcf-compare
  • vcf-isec

and more...

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written by Sophia • Sophia

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!

• 0 views • link
written by Joanne Lim • Joanne Lim

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