Ancestral Sequence

Convert a BAM file to a fasta file using ANGSD. Please see ANGSD's tutorial page for full details on this method.

Basic Usage

To run this method, use the following command

angsd-wrapper Ancestral Ancestral_Sequence_Config

where Ancestral_Sequence_Config is the full path to the configuration file for the 2D site frequency spectrum and Fst estimations.

Input files

All inputs should be specified in Ancestral_Sequence_Config.

Common Variables

This method does not make use of Common_Config.

Method-Specific Variable

This variable is specific to this method:

Variable	Function
ANC_BAM	The full path to the BAM file to be converted

Method Parameters

The parameters for this method can be tweaked as necessary, they have been set for optimal generalized function:

Parameter	Function
DO_FASTA	Convert BAM format to fasta format
DO_COUNTS	Calculate various counts statistics

Output files

To be fixed

• results/TAXON1_Intergenic.arg details of arguments