ANGSD: Analysis of next generation Sequencing Data

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HWE and Inbreeding estimates

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Site estimate of inbreeding coefficient (HWE test)

-HWE_pval_F

By choosing HWE_pval_F 1, no sites will be filtered but the p-value along with the frequency, and F for the sites will be dumped in .hweF.gz file.

Estimation of individual inbreeding coefficients

Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating individual inbreeding coefficients. Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output

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