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 500 target individuals (Both vcf version target.vcf.gz and phase version target.phase.gz are available) using the reference data for local ancestry estimates, including computing LDA, LDAS and AAS. We can paint with the following command:

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

./SparsePainter -reffile donor.vcf.gz -targetfile target.vcf.gz -popfile popnames.txt -mapfile map.txt -namefile targetname.txt -out target_vs_ref -prob -chunklength -chunkcount -aveSNP -aveind -sample

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

./SparsePainter -reffile donor.phase.gz -targetfile target.phase.gz -popfile popnames.txt -mapfile map.txt -namefile targetname.txt -out target_vs_ref -prob -chunklength -chunkcount -aveSNP -aveind -sample

The output file for this example includes target_vs_ref_prob.txt.gz, target_vs_ref_chunklength.txt.gz, target_vs_ref_chunkcount.txt.gz, target_vs_ref_aveSNPprob.txt, target_vs_ref_aveindprob.txt, target_vs_ref_samples.txt.gz and target_vs_ref_fixedlambda.txt.

If you want to compute LDA, LDAS or AAS, simply add -LDA, -LDAS or -AAS at the end of the above commands.