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Question: Subtract one VCF file from another VCF file
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gravatar for ambi1999
2.0 years ago by
ambi1999 • 30
ambi1999 • 30 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 • 1.4k views
ADD COMMENT • link •
modified 2.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.0 years ago by ambi1999 • 30
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gravatar for Jennifer Hillman Jackson
2.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.0 years ago by Jennifer Hillman Jackson ♦ 25k
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