GATK4 CollectHsMetrics - How to avoid the overlap of adjacent intervals ?

psb21psb21 BejaMember
edited February 2018 in Ask the GATK team

Hello,

I'm trying to access the quality of my targeted experiment, and I'm interested on saving the per target information using the --PER_TARGET_COVERAGE argument. However, I observed that when coordinates of the intervals are adjacent, they are merged in the output:

ENSG00000118729.11_CASQ2_exon|ENSG00000118729.11_CASQ2_intron

I want to analyse each target separately, so I tried to add --interval_merging=OVERLAPPING_ONLY option but the argument isn't recognized by the tool:
interval_merging is not a recognized option
Tool returned:
1

How can I avoid this behavior?
Thanks in advance,
Pedro Barbosa

Issue · Github
by Sheila

Issue Number
4439
State
open
Last Updated

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