References

Publications reporting the ANGSD program, detailing the methods used in ANGSD, or testing the accuracy of ANGSD relative to other approaches.

###The paper reporting the ANGSD program:

Korneliussen T, Albrechtsen A, Nielsen R (2014) ANGSD: Analysis of Next Generation Sequencing Data. BMC Bioinformatics 15: 356.

###Methods used in ANGSD are explained in:

Nielsen R, Korneliussen T, Albrechtsen A, Li Y, Wang J (2012) SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data. PLoS One 7: e37558.

###FST and PCA methods are detailed in:

Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, Huerta-Sanchez E, Albrechtsen A, Nielsen R (2013) Quantifying population genetic differentiation from next-generation sequencing data. Genetics 195: 979-992.

###Estimation of individual inbreeding coefficients are detailed in:

Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R (2013) Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Res 23: 1852-1861.

###A comparison of the accuracy of population genetic analyses using ANGSD versus various SNP calling approaches:

Han E, Sinsheimer JS, Novembre J (2014) Characterizing bias in population genetic inferences from low-coverage sequencing data. Mol Biol Evol 31: 723-735.