Question: Need help with "VCF-VCFintersect:" tool
gravatar for ayesha.rasool
4.2 years ago by
United States
ayesha.rasool0 wrote:



Tool name: VCF-VCFintersect:
Tool version: 0.0.2
Tool ID:
ToolShed URL:


I would like to know the format of files for VCF intersect. I have my vcf files with .vcf.txt. I removed the headings and only have list of chromosome numbers and numerical data  in two columns with SNP call. I want to intersect two files but they are not being uploaded. 

I am not sure why am I unable to use this tool.

Ayesha Rasool

snp vcf-vcfintersect: • 1.2k views
ADD COMMENTlink modified 4.2 years ago by Jennifer Hillman Jackson25k • written 4.2 years ago by ayesha.rasool0
gravatar for Jennifer Hillman Jackson
4.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The input for this tool are the original VCF files - unchanged. Make sure that the datatype is assigned as "vcf".

Now, if you just want to intersect data that has been moved away from VCF format (or any text format) into basic tabular format, see the tools under the group "Join, Subtract and Group". 

More complex merging can be done if you have data in interval format (requires chrom, start, end to be specified). Search in the tool box to find tools - are in many categories - or start in the group "Operate on Genomic Intervals"

Datatype help:

Hopefully one of these options will fit your goals! Jen, Galaxy team

ADD COMMENTlink written 4.2 years ago by Jennifer Hillman Jackson25k
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