Sample not being detected as edited despite evidence of editing in the bam file

[alan-tracey]

Description of the bug

I’ve run this pipeline now with a few hundred samples - generally it seems to be working very well. However, I notice that one sample which clearly shows editing in the bam file, is not being detected as edited. Looking at the indels QC file, almost all the reads are not passing filter. However, I can’t see from the bam file why it shouldn’t be passing filter.

Command used and terminal output

No response

Relevant files

No response

System information

No response

[alan-tracey]

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