I am trying to extract variant reads for deletion (large SVs) from DNA-seq bam files. In IGV, variant reads for deletions are labelled in red (insert size larger than expected): IGV link. I am currently using the pysam package to parse bam files. I have a look at those deletion variant reads in red, but couldn't find unique features to extract them out from the bam files...not sure how IGV identifies those reads. Any suggestions? Thanks!