IGV 2.17.3

[Robin Everts]

Hello all:

I have a weird issue.

For some reason in IGV 2.17.3 I cannot see alignments in a 1 Mb section of my genome (equcab3). The rest of the genome I can view without a problem.

I know the calls are there as the pipeline has outputted the right calls.

Is there a way to mask alignments in a certain sections of the genome? And did I invoke that accidentally? I do not see anything in the manual about it.

Any help would be appreciated!

Cheers,

Robin Everts

[igv-help]

There's no way to mask a region.    Can you see the alignments with another tool,  like samtools tview?