ANGSD: Analysis of next generation Sequencing Data

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Error estimation

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Error estimation from polymorphic sites

Kim et al.

Citation

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