Question: Subtract one VCF file from another VCF file
0
gravatar for ambi1999
22 months ago by
ambi199930
ambi199930 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 • 1.2k views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson25k • written 22 months ago by ambi199930
0
gravatar for Jennifer Hillman Jackson
22 months ago by
United States
Jennifer Hillman Jackson25k 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 22 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 126 users visited in the last hour