ANGSD: Analysis of next generation Sequencing Data
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Heterozygosity: Difference between revisions
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This is simply the [[SFS Estimation]] for single samples. | This is simply the [[SFS Estimation]] for single samples. | ||
A short example is: | A short example is: | ||
<pre> | <pre> | ||
./angsd -i my.bam -anc ancestral.fa -dosaf 1 -gl 1 | |||
#OR | |||
./angsd -i my.bam -anc ref.fa -dosaf 1 -fold 1 | |||
</pre> | </pre> | ||
=Local estimate= | =Local estimate= | ||
Revision as of 16:26, 10 January 2017
The heterozygosity is the proportion of heterozygous genotypes.
This can either be a global estimate or a local estimate.
For diploid single samples the hetereo zygosity is simply second value in the SFS/AFS. An important aspect with this approach is that we DO NOT require to fix the major and minor. By fixing the ancestral we loop over the 3 possible derived alleles, or we can use the reference as the ancestral and fold the spectrum.
Global estimate
This is simply the SFS Estimation for single samples. A short example is:
./angsd -i my.bam -anc ancestral.fa -dosaf 1 -gl 1 #OR ./angsd -i my.bam -anc ref.fa -dosaf 1 -fold 1