Answers.Body: <p>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 <a href="http://bio-bwa.sourceforge.net/bwa.shtml" rel="nofollow noreferrer">manual page</a>.</p>
  
  <p>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.</p>
  
  <p>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.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-30T23:10:24.257Z
Answers.LastActivityDate: 2019-04-30T23:10:24.257Z
Answers.UserDisplayName: Mehrdad Bakhtiari
Body: <p>How can I detect a split read in a BAM file?
  Is there any sign in the CIGAR string that describes split read? </p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-19T14:27:34.220Z
Comments.Text: 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?
Comments.UserDisplayName: Bioathlete
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-19T14:46:50.607Z
Comments.Text: yes, for example this site " https://galaxyproject.org/tutorials/ngs/" describes SAM/BAM file structer but i want know what is "split read" and how reported in this file?
Comments.UserDisplayName: fatemeh khoramdel
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-19T15:17:55.593Z
Comments.Text: @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?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-19T16:14:14.917Z
Comments.Text: 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
Comments.UserDisplayName: fatemeh khoramdel
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-23T17:45:48.717Z
Comments.Text: 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](https://bioinformatics.stackexchange.com/questions/2702/mark-bwa-sw-split-alignments-in-output-for-long-reads) may be useful for you
Comments.UserDisplayName: James Hawley
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-05-03T15:54:34.263Z
Comments.Text: Hello @fatemehkhoramdel, I find this a nice question. The context you write in comments is very useful, it would be even better if you would [edit] your question and it the info there directly :-).
Comments.UserDisplayName: Kamil S Jaron
Tags: <phylogenetics><sam><structural-variation><cigar>
Title: How do I find split reads?
ThreadText: # How do I find split reads?
  
  (Asked by: username_0 on 2019-04-19)
  
  How can I detect a split read in a BAM file?
  Is there any sign in the CIGAR string that describes split read?
  
  **Tags:** phylogenetics, sam, structural-variation, cigar
  
  > **Comments:**
  > **username_1**: 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?  
  > **username_0**: yes, for example this site " https://galaxyproject.org/tutorials/ngs/" describes SAM/BAM file structer but i want know what is "split read" and how reported in this file?  
  > **username_2**: @username_0 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?  
  > **username_0**: 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  
  > **username_3**: 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](https://bioinformatics.stackexchange.com/questions/2702/mark-bwa-sw-split-alignments-in-output-for-long-reads) may be useful for you  
  > **username_4**: Hello @username_0, I find this a nice question. The context you write in comments is very useful, it would be even better if you would [edit] your question and it the info there directly :-).  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_5 on 2019-04-30. Score: 3
  
  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](http://bio-bwa.sourceforge.net/bwa.shtml).
  
  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.
  
  
  ---
  
  