Question: Subtract one VCF file from another VCF file
0
gravatar for ambi1999
14 months ago by
ambi199920
ambi199920 wrote:

Hi,

Is there a way in Galaxy to subtract one VCF file from another to get a VCF file containing just the SNPs unique to one of the samples?

I have tried Subtract Whole Dataset under 'Join, Subtract and Group' but it does not seem to work give me the correct answer.

ps: I know subtract in bedtools will work but I am looking for a tool in galaxy.

Cheers, Ambi.

snp vcf • 632 views
ADD COMMENTlink modified 14 months ago by Jennifer Hillman Jackson23k • written 14 months ago by ambi199920
0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

Please see the tools in the group NGS: VCF Manipulatinon. Try VCF Intersect with the -v (invert) and -i (intersection) options. Run twice to find the novel data in each as the output will represent novel content in the first input dataset entered on the tool form.

https://github.com/vcflib/vcflib#vcfintersect

That said, BedTools is wrapped in Galaxy, if you want to use those tools instead (have transformed the VCFs to tabular/bed format).

Hope this helps, Jen, Galaxy team

ADD COMMENTlink written 14 months ago by Jennifer Hillman Jackson23k
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