SplitIntervals GATK4 merging bug
I'd like to report a bug in the SplitIntervals task, using the latest version - GATK4 126.96.36.199. The argument:
fails to prevent the merging of adjacent intervals, such that
1 874168 874582 + CEX-chr1-874418-874511 1 874583 875092 + CEX-chr1-874653-874842
1 874168 875092 + .
I need these intervals to be separate intervals, and this argument clearly doesn't work.
This is causing severe problems with our CNV workflows, and we'd like to be able to use this task to scatter across intervals. For some reason, I can't upload .zip or .tsv files, so if we agree this is a bug, then I could submit a bug report as described in Article#1894.
Thank you so much.