# Maximum Number of Mismatches

`CalcMaxMismatch.Rd`

Calculate the maximum expected number of mismatches for duplicate samples, parent-offspring pairs, and parent-parent-offspring trios.

## Arguments

- Err
estimated genotyping error rate, as a single number or 3x3 matrix (averaged value(s) across SNPs), or a vector with the same length as MAF, or a nSnp x 3 x 3 array. If a matrix, this should be the probability of observed genotype (columns) conditional on actual genotype (rows). Each row must therefore sum to 1. If an array, each 3x3 slice should abide this rule.

- MAF
vector with minor allele frequency at each SNP.

- ErrFlavour
function that takes

`Err`

as input, and returns a 3x3 matrix of observed (columns) conditional on actual (rows) genotypes, or choose from inbuilt ones as used in sequoia 'version2.0', 'version1.3', or 'version1.1'. Ignored if`Err`

is a matrix. See`ErrToM`

.- qntl
quantile of binomial distribution to be used as the maximum, of individual-level probability. For a desired dataset-level probability quantile \(Q\), use

`qntl`

\(= Q^{(1/N)}\), where \(N\) is the number of individuals.

## Value

A vector with three integers:

- DUP
Maximum number of differences between 2 samples from the same individual

- OH
Maximum number of Opposing Homozygous SNPs between a true parent-offspring pair

- ME
Maximum number of Mendelian Errors among a true parent-parent- offspring trio

.

## Details

The thresholds for maximum number of mismatches calculated here aim
to minimise false negatives, i.e. to minimise the chance that any true
duplicates or true parent-offspring pairs are already excluded during the
filtering steps where these `MaxMismatch`

values are used.
Consequently, there is a high probability of false positives, i.e. it is
likely that some sample pairs with fewer mismatches than the
`MaxMismatch`

threshold, are in fact not duplicate samples or
parent-offspring pairs. Use of these `MaxMismatch`

thresholds is
therefore only the first step of pedigree reconstruction by
`sequoia`

.