ANGSD: Analysis of next generation Sequencing Data
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Error estimation: Difference between revisions
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=Error estimation from polymorphic sites= | =Error estimation from polymorphic sites= | ||
The method for estimating typespecific errors is described in [[Kim2011]], and is based on the ''counts'' of the 4 different nucleotides. This method should be applied to the site that are variable and the measure for variability is the simple MAF estimator that is described in [[Li2010]]. | |||
[[Kim11|Citation]] | [[Kim11|Citation]] | ||
Revision as of 22:32, 11 October 2012
Error estimation from polymorphic sites
The method for estimating typespecific errors is described in Kim2011, and is based on the counts of the 4 different nucleotides. This method should be applied to the site that are variable and the measure for variability is the simple MAF estimator that is described in Li2010.
Error estimation using an outgroup and an error free individual
- -doAncError [int]
- -anc [filename]
fasta file with the ancestral alleles
- -ref [filename]
fasta file of a reference (error free) individual.
- -doAncError 1
- -doAncError 2
additional options
- -minQ [int]
default 0. Minimum allowed base quality score
- -minMapQ [int]
default 0. Minimum allowed mapping quality score