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
Kim et al.
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