Penetrance table model

In this tutorial, we will use SeqSIMLA to simulate families with disease.

• In this tutorial, we use Asian 500kb on chrom 1(download).
  -popfile ASN_500k.bed.gz
  -recfile ASN_500k.rec
  
  
• In our example pedigree file(download), there are 20 families, with 1,380 people.
  We randomly choose two persons from each of the pedigrees in the pedigree file, then put them in a proband file(download).
  -famfile SAP.txt
  -proband probands.txt
  
  If you don't have a pedigree file, you can just use the option "default 3-generation families" to generate fixed 3-generation pedigrees.
  see "Output Options: -fam number" in User Manual.
  
  
• One replicate of simulated data.
  -batch 1
  
  
• To generate the disease status by the penetrance table model with a penetrance table file(download).
  -penfile pen.txt
  
  or to simulate gene-gene interactions with this penetrance table(download).
  -penfile pen_gg.txt

Collect all file into a folder and placed in the same directory you run SeqSIMA

Execute the following command,
./SeqSIMLA -popfile data/ASN_500k.bed.gz -recfile data/ASN_500k.rec -famfile data/SAP.txt -proband data/probands.txt -folder test1 -header test -batch 1 -site 1,200,3000 -penfile data/pen.txt

With our example files, this simulation would take about 150 seconds.

Notice: If you don't want to make the command yourself, we provide a generate command user interface on our website.