Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Need help with "VCF-VCFintersect:" tool
0
gravatar for ayesha.rasool
4.2 years ago by
ayesha.rasool • 0
United States
ayesha.rasool • 0 wrote:

 

 

Tool name: VCF-VCFintersect:
Tool version: 0.0.2
Tool ID: toolshed.g2.bx.psu.edu/repos/anton/vcfvcfintersect/vcfvcfintersect/0.0.2
ToolShed URL: https://toolshed.g2.bx.psu.edu/view/anton/vcfvcfintersect

Hello, 

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 COMMENT • link •
modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by ayesha.rasool • 0
1
gravatar for Jennifer Hillman Jackson
4.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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:
http://wiki.galaxyproject.org/Learn/Datatypes

Hopefully one of these options will fit your goals! Jen, Galaxy team
ADD COMMENT • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour