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. here. 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
You'd have to show us what probes.txt is supposed to look like. A BED file is just a text file, so perhaps it's already formatted for your needs.
Hi!
Taken from Conifer documentation: