The example dataset is available on GitHub. This example includes 8000 reference individuals from 4 populations with 2091 SNPs (Both vcf version donor.vcf.gz and phase version donor.phase.gz are available), and the aim is to paint them against themselves for admixture estimation. We can paint with the following command:

  • If your input file is in vcf or vcf.gz format:

./SparsePainter -reffile donor.vcf.gz -targetfile donor.vcf.gz -popfile popnames.txt -mapfile map.txt -namefile refname.txt -out ref_vs_ref -prob -chunklength -chunkcount -loo

  • If your input file is in phase or phase.gz format:

./SparsePainter -reffile donor.phase.gz -targetfile donor.phase.gz -popfile popnames.txt -mapfile map.txt -namefile refname.txt -out ref_vs_ref -prob -chunklength -chunkcount -loo

The output file for this example includes ref_vs_ref_prob.txt.gz, ref_vs_ref_chunklength.txt.gz, ref_vs_ref_chunkcount.txt.gz and ref_vs_ref_fixedlambda.txt.