RFMix does not necessary start the ancestry windows where the input VCF does. Currently, the ExtractTracts.py script will read through the entire msp file if the first sites in the input VCF is before the msp windows start. It will then use the last windows ancestry calls as the ancestry calls for all sites. This fixes the bug by skipping the VCF site if it is before the first windows start.
RFMix does not necessary start the ancestry windows where the input VCF does. Currently, the ExtractTracts.py script will read through the entire msp file if the first sites in the input VCF is before the msp windows start. It will then use the last windows ancestry calls as the ancestry calls for all sites. This fixes the bug by skipping the VCF site if it is before the first windows start.