How do I detect deletions?

1

Hi there, I have been working on this project with DNA-seq samples from E.coli data. I am trying to see if there are any indels or deletions on a small contig in the .fa file and I viewed one of my BAM files in IGV. Below is a screenshot.

enter image description here

In the IGV manual, it says the red pairs are deletions. I have tried to use bcftools mpileup and bcftools call to identify these deletions but am having no success. I have also tried freebayes and HaplotypeCaller and still have no success. Any help is appreciated.


bcftools


DNA-seq


calling


variant

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