errors in wes-pairs-cnv pipeline

[stevekm]

When trying to run the wes-pairs-cnv pipeline, I get the following errors:

logs-qsub/sns.wes-pairs-cnv.SeraCare-1to4-Positive-HapMap-B17-1267.o3950853: get-set-setting.sh ERROR: the value for setting EXP-PROBES-BED must be specified
logs-qsub/sns.wes-pairs-cnv.SeraCare-1to4-Positive-HapMap-B17-1267.o3950853: cnvs-wes-freec.sh ERROR: BED  DOES NOT EXIST

What .bed file is being referenced here and how should it be set?

[igordot]

You need a BED file for the probes. You can add it to the project directory like the targets BED.

[stevekm]

The .bed file was present:

example_sns_analysis5$ ll NGS580_targets.bed
-rw-r----- 1 kellys04 molecpathlab 565K Oct 24 17:22 NGS580_targets.bed

[igordot]

You need a BED file for targets (present) and probes. Two separate files.

[stevekm]

How are you supposed to set up the different .bed files so the program knows which is which?

[igordot]

The one for probes should say "probes" in the file name. In my personal experience, that has always been the case with the files provided by the manufacturer.