Ancestral Sequence

ANSGD BAM to Fasta conversion. See ANGSD for full details on this method.

To use this method, you would run:

bash ./scripts/FASTA.sh ./scripts/

with the proper taxon name filled in.

Input files

Scripts

• Script filename: FASTA.sh
• example configuration file: .conf

Necessary input files

• data/TAXON1_samples.txt bam list

Output files

• results/TAXON1_Intergenic.arg details of arguments

Mandatory 2DSFS_TAXON1.TAXON2.conf variables

• TAXON1 first taxon name

Optional 2DSFS_TAXON1.TAXON2.conf variables

• DO_SAF creates SFS (default=2)