How can I detect a split read in a BAM file? Is there any sign in the CIGAR string that describes split read?

  • 2
    $\begingroup$ Welcome to the forum. Have to done any research on this topic? Have you looked into secondary and/or supplementary alignments? What aligner was used to generated the BAM file? $\endgroup$
    – Bioathlete
    Apr 19, 2019 at 14:27
  • $\begingroup$ yes, for example this site " galaxyproject.org/tutorials/ngs" describes SAM/BAM file structer but i want know what is "split read" and how reported in this file? $\endgroup$ Apr 19, 2019 at 14:46
  • $\begingroup$ @fatemehkhoramdel That answers (to an extent) the question on "have you done any research?". Can you also answer the questions on secondary/supplementary alignments and the tool used to generate the BAM please? $\endgroup$
    – Ram RS
    Apr 19, 2019 at 15:17
  • $\begingroup$ If i understand this question correctly, you can look at "The Sequence Alignment/Map format and SAMtools" at google scholar. otherwais i don't know about it $\endgroup$ Apr 19, 2019 at 16:14
  • 1
    $\begingroup$ It's easier to help you if you provide a small amount of background info in your question to see what you know and what work you've done so far. Another good first thing to do is to search the Bioinformatics StackExchange to see if a similar question has been asked before. In your case, it looks like this question may be useful for you $\endgroup$ Apr 23, 2019 at 17:45

1 Answer 1


The answer to this question depends on the aligner used to generate SAM/BAM file. For BWA method that is part of the pipeline mentioned in comments, split reads will be flagged as supplementary alignment (2048). You can modify this behavior by using option -M as described in the BWA-MEM manual page.

So, in case of split alignment, you will end up with multiple aligned segments that have identical query name and they are flagged as 2048. These segments may only have part of the original read sequence, but the complete read sequence is present in at least one of the segments.

Also, there is no unique sign in CIGAR of an individual segment to identify split reads. Each aligned segment of the original read may have long deletion in its CIGAR or aligned pairs. However, without looking at all segments with the read ID it is not clear whether the segment has a novel sequence in it that doesn't align with reference or that part matches different chromosome/coordinates.


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