How chimeric reads are identified is described in 'chimeric_reads'. The indices returned will be the proportion of reads with any of the features above. The user also has the option to only check for 1 of the 2.
chimeric_proportion(bamfile, checks = 3)
the path to the BAM file
1 indicates checking only for SA tag, 2 only for rname, and 3 for both. Default is both.
NOTE that the absence of either of the 2 features above does NOT mean that your alignment does not have chimeras, especially if you are using older versions of reference aligners. This is merely a heuristic diagnostic using convenient metrics to assess overall quality of your alignment.
Planned improvements: Also check for if the 0x800 flag exists, indicating a supplementary and thus chimeric alignment. This flag only exists in version 1.5 of the SAM and BAM formats and beyond.
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