ANGSD: Analysis of next generation Sequencing Data

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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'
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