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I tried to follow the instructions for targeted NGS here using amber 3.9.1 and cobalt 1.15.2. Unfortunately I'm getting a null pointer exception from the Normalisation step with little explanation. Would appreciate help diagnosing the issue.
I tried updating the tools but I'm still seeing the same error message. I also noticed -target_regions_bed has been added to the list of amber's options in the latest release and wasn't sure if that needed to be part of the process? But when I tried to pass it, it immediately failed:
10:28:29.569 [INFO ] Amber version 4.0
10:28:39.814 [ERROR] failed to load target regions file(): targets.bed
Hello, I was getting the same error here. I noticed that my bed file contained some ALT contigs (e.g., chr7_KI270803v1_alt), and removing those from the file solved the problem in my case. I don't know if ALT contigs are anyway ignored in analysis but in that case they should be handled. Though not sure if the original problem in the issue was this.
Hello,
I tried to follow the instructions for targeted NGS here using amber 3.9.1 and cobalt 1.15.2. Unfortunately I'm getting a null pointer exception from the Normalisation step with little explanation. Would appreciate help diagnosing the issue.
Command:
Stderr:
There is nothing special about my target BED:
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