ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
Direct Ancestry
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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'