Based on the 2dsfs for two individuals it is possible to estimate the direct ancestry
angsd -i ind1.bam -gl 1 -anc ancestral.fasta -dosaf 1 -out ind1 angsd -i ind2.bam -gl 1 -anc ancestral.fasta -dosaf 1 -out ind2 realSFS ind1.saf.idx ind2.saf.idx -P 32 >2dsfs Rscript direct_ancestry.R sfsfile='2dsfs'
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ANGSD
Pages
Population genetics
Population structure
Medical genetics
IBD/IBS
Summaries
SNPs and genotypes
Output
Misc/util programs
Program structure
About ANGSD