Covert .BED file to probes.txt file ?

Question

[stevenlang123]

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

[Devon Ryan]

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.

[stevenlang123]

Hi!

Taken from Conifer documentation:

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

Answer 1

[Devon Ryan]

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.

[stevenlang123]

Thank you Devon! Your help is greatly appreciated as I am a noob at using computational tools.

[jftchau]

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.