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SplitIntervals GATK4 merging bug

ncamardancamarda DFCIMember, Broadie

Hello,

I'd like to report a bug in the SplitIntervals task, using the latest version - GATK4 4.0.4.0. The argument:

--interval-merging-rule OVERLAPPING_ONLY

fails to prevent the merging of adjacent intervals, such that

1       874168  874582  +       CEX-chr1-874418-874511
1       874583  875092  +       CEX-chr1-874653-874842

becomes

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.

Best,
Nick

Answers

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