Does anyone know of a tool to convert a .BED file to a probes.txt file?

This file defines the chr:start-stop coordinates for the probes/targets in the exome capture. We suggest basing this off the published target files from the vendor, but a custom file may be necessary for some designs. You can download the standard probe file used in Krumm et al. <a href="http://sourceforge.net/projects/conifer/files/probes.txt/download">here</a>. Otherwise, the probes.txt file should be a tab-delimited file with the following header and columns:

    chr	start	stop	name
    1	69090	70008	OR4F5
    1	565876	566576	
    1	801642	802733	
    1	861321	861393	SAMD11
    1	865534	865716	SAMD11
    1	866418	866469	SAMD11
    1	871151	871276	SAMD11
    1	874419	874509	SAMD11
    1	874654	874840	SAMD11
Thanks for updating your post. Just take the first 3 columns of the BED file and add a header. You might need to add an empty 4th column, try it and see. You can always annotated the BED file (have a look at bedtools) if conifer complains about an empty 4th column.