This is the default method to call genotypes from a table of variant counts. Methods:-
Three sequential steps for each marker/sample pair:
if the number
of reads is less than
minTotalReads the genotype
if the difference
between the sum of counts of the top two variants and the
count of the third most variant, expressed as proportion
of total, is less than
minDiffToVarThree, OR the
third most abundant variant accounts for more than
maxPropVarThree (default=0.1) of the reads, then the
genotype is ‘complexVars’
difference between the counts of top two variants,
expressed as a proportion of the total, is greater than
or equal to
minPropDiffHomHetThreshold, then the
genotype is HOMOZYGOTE. Otherwise it is
1 2 3 4
The table of sequence counts as in the markerSampleTable of an mlgtResult object.
Minimum number of reads before attempting to call genotypes
Difference between sum of counts of top two variants and the count of the third most frequent variant, expressed as proportion of total.
Difference between counts of top two variants. One way to distinguish HOMOZYGOTES and HETEROZYGOTES.
Also call as 'complexVars' if the third variant accounts for more than this proportion of used reads (default=0.1)
A data.frame identical to those in markerSampleList but with additional columns giving parameter values, and a 'status' column giving the genotype status.
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