Regionfile

When your inputfile is bam files, then you can specify region

You can specify a specific region using the following 3 ways:

./angsd -bam bamfiles.list -r chr20:
./angsd -bam bamfiles.list -r chr20:-2000000
./angsd -bam bamfiles.list -r chr20:2000000-
./angsd -bam bamfiles.list -r chr20:1000000-2000000

1. all chr20 2. from beginning of chr20 to position 2000000 3. from position 2000000 to the end of chr20 4. from posiiton 1000000 to position 2000000 in chr20.

If you have more than one region of interest then you can supply a file containing your regions, one per line.

./angsd -bam bamfiles.list -rf region.file