Merging VCF files

usegalaxy.eu support
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1

Hi,

I am hoping someone can give me a tool recommendation for the following task.

I have generated multiple vcf files and now I want to combine them into one, while eliminating duplicates (variants present in more than one file). However while doing this, I also want data on how many files a given variant was present in.

As far as I know tools like vcf-merge, Combine Variants etc does not provide this information. Is this possible?

Any help is greatly appreciated! Thank You.

@jennaj @wm75 @mvdbeek @jxtx

2

Hi , i need to combine variants and its showing requirement of version 1.4 whereas in galaxy its 0.0.4 how to do this, please help and suggest. Did you got the answer and do you mind sharing. I am stuck

4

Find most tools in the tool panel section: VCF/BFC

There are many ways to add in sample names, merge, and similar functions.

GTN Tutorials cover analysis methods