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 | 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 sites that are variable and the measure for variability is the simple MAF estimator that is described in [[Li2010]]. | ||
[[ | ==options== | ||
; -cutoff [float] | |||
default 0.02. This means we only run the error estimation on sites with a MAF>0.02. | |||
; -errors [filename] | |||
This file should contain a guess of the typespecific errors. NB this is not implemented in the current version | |||
==example== | |||
=Error estimation using an outgroup and an error free individual= | =Error estimation using an outgroup and an error free individual= | ||
Revision as of 22:35, 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 sites that are variable and the measure for variability is the simple MAF estimator that is described in Li2010.
options
- -cutoff [float]
default 0.02. This means we only run the error estimation on sites with a MAF>0.02.
- -errors [filename]
This file should contain a guess of the typespecific errors. NB this is not implemented in the current version
example
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