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IGV deletion insert size

Hi,

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!

deletion igv variantion structural dna
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written by robinycfang • robinycfang

1 answer

but couldn't find unique features to extract them out from the bam files...

  • reads not-properly-paired with a large TLEN (distance) between the read and it's mate.
    • reads with supplementary alignments mapping far from the original read.
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks! This gave me some ideas! I guess I will start working on measuring the inner distance between two paired reads (segments), and if the inner distance is unexpected large (e.g., >>100bp), then they are potential variant reads. Is that correct?

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written by robinycfang • robinycfang

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