To extract maf and gather all pop maf in one file
it will also output the list of snps for which maf was calculated in all populations (represented by the min % of IND given as filter. The out put is in 02_raw_data
You can also proceed straight to formatting maf for various analyses. This extracts the maf and gathers all pop maf in one file (same as above)+ format them for rda & various analysis in their respective folders. It will aslo output in the list of snps in 02_raw_data
ANGSD_PATH=../angsd_pipeline/
POP1_FILE=$ANGSD_PATH/02_info/pop.txt
source $ANGSD_PATH/01_scripts/01_config.sh
Rscript 01_scripts/Rscripts/extract_format_maf.r "$MIN_MAF" "$PERCENT_IND" "$POP1_FILE" "$ANGSD_PATH"
The next step would be to format the environment file for the different analyses. I have uploaded an example in each subfolder