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Identify similarly mapped reads in BAM/SAM?

I have a BAM (or SAM) file of reads mapped to a reference genome.

I would like to identify which reads are mapped similarly/to approximately the same location, which reads might be "orthologs".

For example, when visualizing the BAM file in IGV, the two reads circled in the orange are similar.

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How can I parse this information from a BAM or SAM file? Using Python or R?

bam igv sam python r
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written by Eliveri • Eliveri

1 answer 

 bedtools bamtobed -i in.bam | datamash -g 1,2,3  collapse 4
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written by Pierre Lindenbaum Pierre Lindenbaum

Thank you! This is a great and straightforward solution.

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written by Eliveri • Eliveri

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