Welcome to iDentification of pIG breeds (iDIGs) v2.0 !

iDIGs is a tool for global pig breed identification. Our database has 3,622 samples and 124 breeds worldwide. Now, iDIGs has two mian functions: pig breed identification and panel design for specific breeds identification.

1. Breed Identification
2. Panel Design

1. Breed Identification

Using our database to recognize users' pig breed

• Step1: Choose the version of your reference pig genome (10.2 or 11.1) and upload your PLINK binary file. No missing SNPs are allowed . You can perform imputation using PHARP or Beagle.
• Step2: Choose reference breeds ( Optional ). If not chose, all breeds in our database will be used as reference.
• Step3: Input your E-mail address and submit. The results will send to the E-mail address automatically.
• Results: A table of two columns. The first column is the input sampleID. The second column is the putative breed label.

2. Panel Design

Designing a small panel to distinguish some specific breeds from each other.

• Step1: Choose the version of your reference pig genome (10.2 or 11.1) and the SNP number in the panel. Note that, the SNP number should be less than 10,000.
• Step2: choose breeds you want to distinguish from. You can select multiple breed IDs or a single breed ID. If you input multiple breed IDs, markers that can distinguish all input breeds from each other will be selected. If you input a single breed ID, Markers that can distinguish your input breed from all other breeds in our database will be selected.
• Step3(non-essential):If you want to use the breeds you have for panel design, you can upload your BIM file and frq.strat file .
• Step4: Input your E-mail address and submit. The results will send to the E-mail address automatically.

Results:

• Marker ID used in panel;
• Performance estimation of the panel using 5-fold CV ( Only fully use the breed in iDIGs's database ).

The preformance can be imporved by increasing the SNP number.

Q: What type of data may i uploaded when using iDIGs?

A: We recommand commercial SNP Chips and WGS.

Q: How could i upload big PLINK binary files, such as SNPs from WGS data?

A: Big data (file size > 1 GB), such as WGS data, is hardly upload. Thus, you can download our markerID and only extract overlapped markers to upload, The relevant commands are as follows:

# If using LINUX
chmod +x MakeSNPidL

# Normalize your markerID in bim file and copy files
MakeSNPidL your.bim your.tmp.bim
cp your.bed your.tmp.bed
cp your.fam your.tmp.fam

# Extract overlapped SNPs
plink --bfile your.tmp --extract MarkerID_11.txt --make-bed --out your_filename

Q:How to generate the files(.frq.strat file) required by the panel design module?

A:The relevant commands are as follows:

# Run iDIGs with file.tmp.bed(bim,fam)
# The cluster file is the first two columns of information for your fam file
plink --bfile your_filename --freq --allow-extra-chr --within cluster.txt --out upload

You can also click this specific example when you have problems processing files.

Tips : The principle is to use the user's SNPs that are the same as those in the database samples for panel design,so it is necessary to extract the repeated SNPs.

Any questions, bug reports and suggestions can be posted to E-mail: pan_idigs@163.com .

If you find the results useful, please also help spread the word by sharing about the iDIGs on Twitter, Reddit, or any other social media platform you regularly use.

This software is intended for academic use only and not for commercial use. We are not legally responsible for any unauthorized commercial application.