FSTwindows

Calculate FST values across sliding windows

Example

Name_tab_Lineage.tab contains:

isolate1 ST1 isolate2 ST1 isolate3 ST2 isolate4 ST2 isolate5 ST2 isolate6 ST3

etc,

To compare ST1 to ST2:

perl VCF-multi-sample-to-FST-windows.pl -a Name_tab_Lineage.tab -v Multi_sample.VCF -c ST1 -d ST2 -r reference.fasta > out.window-10kb.tab

Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
modules		modules
LICENSE		LICENSE
README.md		README.md
VCF-multi-sample-to-FST-windows.pl		VCF-multi-sample-to-FST-windows.pl
VCF_to_FST_windows.pl		VCF_to_FST_windows.pl
VCF_to_FST_windows_limited_memory.pl		VCF_to_FST_windows_limited_memory.pl