ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
Error estimation
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