Early farmers from across Europe directly descended from Neolithic Aegeans
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"Early farmers from across Europe di..." refers methods in this paper
...All sequences were aligned against the human reference build GRCh37/hg19 using BWA (35) and realigned using the Genome Analysis Toolkit (36) (SI Appendix, SI3....
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20,557 citations
"Early farmers from across Europe di..." refers methods in this paper
...Following GATK [116], we calculate the Phred-scaled quality of the call as the likelihood difference ∆LL between the ML and the second most likely genotype....
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...Here we adopt a similar strategy as implemented in the Base Quality Score Recalibration (BQSR) tool available in GATK [116], but extend it to ancient DNA by incorporating post-mortem damage....
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13,111 citations
"Early farmers from across Europe di..." refers methods in this paper
...We employ the classic substitution model by Felsenstein [118], which expresses the probability of each genotype gi as a function of π and the substitution rate θ = 2Tμ along the genealogy connecting the two alleles of an individual, where T corresponds to the time to the most recent common ancestor of the two lineages and μ the mutation rate....
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12,661 citations