Predicted Sweep Status will appear here
Sweep Discovery Tool
Background
Selective Sweep is a biological phenomenon in which genetic variations among neighbouring the beneficial mutant allele are swept away due to the effect of genetic hitchhiking.Selective sweep has vast importance in genomic studies related to phylogeny, development of new varieties, disease and pathogen genomics etc.
About Sweep Discovery Tool
“Sweep Discovery Tool” is a user friendly tool for detecting selective sweep in genomic regions. It uses Random Forest based machine learning approach to predict selective sweep from VCF files as an input.
Instructions for Users
- File Format: Provide the input file in .vcf.gz (gzipped VCF format) and .vcf.gz.tbi (tabixed VCF format). Please use valid VCF files with proper information of samples.
- Input Parameters:Provide input files along with other mandatory input parameters such as Chromosome No, Starting Position and Ending Position of the region of interest of the concerned Chromosome.
- Input Details: After providing all the input files save them in a directory by "Save" button and then put other parameters and run the "Predict" button for selective sweep prediction.
Copyright © 2023 ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012. All rights reserved.
Copyright © 2023 ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012. All rights reserved.
Download Datasets
Example Dataset Details
The dataset consist of three files in zipped format where one is VCF file in .vcf format, second one is VCF file in .vcf.gz format and third one is tabixed VCF file in vcf.gz.tbi format. Users are suggested to use those .vcf.gz and .vcf.gz.tbi formatted files as input after extraction. To put the Chromosome No, Start Position and End position of the chromosome users are suggested to view the VCF file in .vcf format only.
Example Input
Please download the example file by clicking the “Download Zipped File” below:
Copyright © 2023 ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012. All rights reserved.
Download Zipped File
Abhik Sarkar
M.Sc. Scholar
Discipline of Bioinformatics
ICAR-Indian Agricultural Research Institute
Pusa, New Delhi, Delhi- 110012, India.
Contact mail: abhik.jenkins.sarkar[at]gmail.com
Dr.Dwijesh Chandra Mishra
Senior Scientist
Division of Agricultural Bioinformatics
ICAR-Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi, Delhi-110012, India.
Contact Mail: dwijesh.mishra[at]icar.gov.in
Dr.Girish Kumar Jha
Head and Principal Scientist
Division of Agricultural Bioinformatics
ICAR-Indian Agricultural Statistics Research Institute
Pusa, New Delhi, Delhi- 110012, India.
Dr.Krishna Kumar Chaturvedi
Principal Scientist
Division of Agricultural Bioinformatics
ICAR-Indian Agricultural Statistics Research Institute
Pusa, New Delhi, Delhi- 110012, India.
Dr. Sanjeev Kumar
Scientist
Division of Agricultural Bioinformatics
ICAR-Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi, Delhi-110012, India.
Dr. Shashi Bhushan Lal
Principal Scientist
Division of Agricultural Bioinformatics
ICAR-Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi, Delhi-110012, India.
Dr. Ranjit Kumar Paul
Senior Scientist
Division of Statistical Genetics
ICAR-Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi, Delhi-110012, India.
Dr. Neeraj Budhlakoti
Scientist
Division of Agricultural Bioinformatics
ICAR-Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi, Delhi-110012, India.
Dipro Sinha
Ph.D. Scholar
Discipline of Bioinformatics
ICAR-Indian Agricultural Research Institute
Pusa, New Delhi, Delhi- 110012, India.
Copyright © 2023 ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012. All rights reserved.
Contact Details
Professor
Discipline of Bioinformatics, Graduate School
ICAR-Indian Agricultural Research Institute
Pusa, New Delhi-110012
Mail Id: alka.arora@icar.gov.in
Director, ICAR-IASRI
ICAR-Indian Agricultural Statistics Research Institute
Pusa, New Delhi-110012
Mail Id: director.iasri@icar.gov.in
Head
Division of Agricultural Bioinformatics
ICAR-Indian Agricultural Statistics Research Institute
Pusa, New Delhi-110012
Mail Id: hd.cabin@iasri.res.in
Copyright © 2023 ICAR-Indian Agricultural Statistics Research Institute, New Delhi-110012. All rights reserved.