README.md

This is a set of tools I find helpful for working with whole genome alignments stored in the SAM format.

The programs are:

• samToBed - This version of a sam <-> bed converter allows the calculation of identity
• samToDot - Create a file that may be rendered into a dotplot using RenderPlot.R
• samLiftover - Transform coordinates from the query genome to target using the SAM file as a mapping.