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comparison PsiCLASS-1.0.2/samtools-0.1.19/bcftools/README @ 0:903fc43d6227 draft default tip

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author lsong10
date Fri, 26 Mar 2021 16:52:45 +0000
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1 The view command of bcftools calls variants, tests Hardy-Weinberg
2 equilibrium (HWE), tests allele balances and estimates allele frequency.
3
4 This command calls a site as a potential variant if P(ref|D,F) is below
5 0.9 (controlled by the -p option), where D is data and F is the prior
6 allele frequency spectrum (AFS).
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8 The view command performs two types of allele balance tests, both based
9 on Fisher's exact test for 2x2 contingency tables with the row variable
10 being reference allele or not. In the first table, the column variable
11 is strand. Two-tail P-value is taken. We test if variant bases tend to
12 come from one strand. In the second table, the column variable is
13 whether a base appears in the first or the last 11bp of the read.
14 One-tail P-value is taken. We test if variant bases tend to occur
15 towards the end of reads, which is usually an indication of
16 misalignment.
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18 Site allele frequency is estimated in two ways. In the first way, the
19 frequency is esimated as \argmax_f P(D|f) under the assumption of
20 HWE. Prior AFS is not used. In the second way, the frequency is
21 estimated as the posterior expectation of allele counts \sum_k
22 kP(k|D,F), dividied by the total number of haplotypes. HWE is not
23 assumed, but the estimate depends on the prior AFS. The two estimates
24 largely agree when the signal is strong, but may differ greatly on weak
25 sites as in this case, the prior plays an important role.
26
27 To test HWE, we calculate the posterior distribution of genotypes
28 (ref-hom, het and alt-hom). Chi-square test is performed. It is worth
29 noting that the model used here is prior dependent and assumes HWE,
30 which is different from both models for allele frequency estimate. The
31 new model actually yields a third estimate of site allele frequency.
32
33 The estimate allele frequency spectrum is printed to stderr per 64k
34 sites. The estimate is in fact only the first round of a EM
35 procedure. The second model (not the model for HWE testing) is used to
36 estimate the AFS.