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
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stevenlang123
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.
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Devon Ryan
Thank you Devon! Your help is greatly appreciated as I am a noob at using computational tools.
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stevenlang123
Hey, I was wondering how you managed to solve the issue with CoNIFER and the probes.txt. Currently, I am trying to make a probes.txt for the NGS platform we use but I am not sure how to annotate to get the fourth column of genes.
So currently I only have the first 3 columns and if I try to submit that to the program, there is an error message.
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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: