Hi!
I mapped paired end library to a genome. Now I am trying to visualise it via IGV, but I am always getting this message when trying to jump to a certain chromosome: Error encountered querying alignments: java.lang.NullPointerException. Reference genome have 19 chromosomes and a lot of unplaced genomic scaffolds. Jumping to these scaffolds does not cause an error. Only when I am picking a chromosome. Bam file is sorted and indexed, Reference file headers and bam headers are same and in the same order.
Tablet and IGB don't have these problems, but I need to understand why it doesn't work with IGV.
I found a few topics in the internet with the same problem, but didn't find any solution.
Help please.
Thank you.
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