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                                            tfwillems

Problem with read IDs repeated in the same BAM file

@gymreklab @shubhamsaini Could you send me a BAM file that on its own can reproduce this issue?

ALLREADS flag discrepancy

I observed this issue with the latest version released on the website (3.0.3)

ALLREADS flag discrepancy

Is it possible this issue is limited to STRs with a name in the last column of the reference bed? I observed this issue when I was inspecting calls for...