ANGSD: Analysis of next generation Sequencing Data
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HWE and Inbreeding estimates: Difference between revisions
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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 | |||
Latest revision as of 16:59, 7 February 2018
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