Question: Vcftools,--Diff Option
1
gravatar for Joanne Lim
7.8 years ago by
Joanne Lim20
United Kingdom
Joanne Lim20 wrote:

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 matrix comparison vcftools • 5.9k views
ADD COMMENTlink modified 7.8 years ago by Sophia300 • written 7.8 years ago by Joanne Lim20

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?

ADD REPLYlink written 7.8 years ago by Sophia300

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?

ADD REPLYlink written 7.8 years ago by Sophia300
1
gravatar for Sophia
7.8 years ago by
Sophia300
Barcelona
Sophia300 wrote:

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

  • vcf-compare
  • vcf-isec

and more...

ADD COMMENTlink written 7.8 years ago by Sophia300

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!

ADD REPLYlink written 7.8 years ago by Joanne Lim20
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