ANGSD: Analysis of next generation Sequencing Data
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Direct Ancestry: Difference between revisions
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(Created page with "Based on the 2dsfs for two individuals it is possible to estimate the direct ancestry") |
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Based on the 2dsfs for two individuals it is possible to estimate the direct ancestry | Based on the 2dsfs for two individuals it is possible to estimate the direct ancestry | ||
<pre> | |||
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' | |||
</pre> | |||
Latest revision as of 21:33, 8 November 2016
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'