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Calculation of Tajima’s D and other neutrality test statistics from low depth next-generation sequencing data
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Multiple tools exist for assessing contamination levels in haploid chromosomes, both from mitochondrial DNA data and using the X-chromosome in males.
“However, multiple tools exist for assessing contamination levels in haploid chromosomes, both from mitochondrial DNA data (for example schmutzi 189 ) and using the X-chromosome in males (for example ANGSD 190,191 ).”
From Ancient DNA analysis (2021) · cites this paper as [191]
The Methods > Model passage identifies ANGSD as a tool used to calculate genotype likelihoods, not to assess contamination. Searches for contamination and for the male X chromosome found no passage in our copy addressing that use of ANGSD. (LLM, conf=0.76)
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“Pr(D | x = j) can be calculated fast using a dynamic programming algorithm described in detail in references [33,35], and we refer readers to these publications for details.”
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“Early genotype calling methods were based on simple criteria, such as calling a heterozygous site, if the proportion of non-reference alleles is between 20% and 80% [13,14].”
MethodSelf-citationNielsen, R., Korneliussen, T., Albrechtsen, A., Li, Y., & Wang, J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037558 · Cited by 424 · cited 4×
“…will explore for calculating neutrality statistics ( T ) for a region, is to estimate the SFS, η = ( η k ) k =0, … , n , using one of these methods, in this case the maximum likelihood method by [35] ( ^ η ML ), and then calculate T using estimated values of η instead of the (unknown) true values.”
MethodInfluentialSelf-citationGenomic regions exhibiting positive selection identified from dense genotype data
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Metadata
- Authors
- Korneliussen, T. S., Moltke, I., Albrechtsen, A., & Nielsen, R.
- Venue
- BMC Bioinformatics
- Published
- 2013-10-02
- Volume
- 14
- Issue
- 1
- ISSN
- 1471-2105
- PMC
- PMC4015034
- Cited by
- 269
- References
- 9
- Language
- en
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