ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
HWE and Inbreeding estimates: Difference between revisions
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=Site estimate of inbreeding coefficient (HWE test)= | |||
;-HWE_pval | ;-HWE_pval | ||
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By choosing '''HWE_pval 1''', no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in '''.hwe.gz''' file. | By choosing '''HWE_pval 1''', no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in '''.hwe.gz''' file. | ||
=Estimation of individual inbreeding coefficients= | |||
Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work. | Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work. | ||
Filipe G. Vieira has been extending the ANGSD feature set by a very fancy method for estimating 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 | Please see his website here: https://github.com/fgvieira/ngsF for the latest version which is utilising ANGSD output | ||
Revision as of 12:51, 28 February 2014
Site estimate of inbreeding coefficient (HWE test)
- -HWE_pval
By choosing HWE_pval 1, no sites will be filtered but the p-value along wight the frequency, and F for the sites will be dumped in .hwe.gz file.
Estimation of individual inbreeding coefficients
Some parts of the ANGSD code (site frequency-sample allele frequency using genotype likelihoods) will work for inbreeding estimates version 0.572+. Downstream analysis that are using frequencies will therefore work.
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