Body: <p>I saw in the SAM format specifications that the SEQ field (10th column) can be a &quot;*&quot; if the sequence is not stored, instead of being the sequence of the mapped read. Under what circumstances is this expected to occur? I don't understand why it's allowed in the spec.</p>
  <p>For a concrete example, I have pacbio data mapped to a reference sequence, and some of the records in the SAM file have a sequence of *, and I don't know why or if that means anything. I don't understand why they exist, since the data is ostensibly present in the FASTQ file I use as input to the read mapper, and I don't understand what purpose they could have, since it seems to me that these records couldn't be interpreted by variant calling software. At best it would seem they can be used to infer coverage, but it's coverage by sequences of an uncertain nature?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-03T13:27:43.633Z
Comments.Text: Related: [How to output all sequences with bwa mem, not `*`?](https://bioinformatics.stackexchange.com/q/5579/3967)
Comments.UserDisplayName: acvill
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-03T13:30:11.707Z
Comments.Text: Sounds like I should check if these are exclusively secondary alignments
Comments.UserDisplayName: Oakheart
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-03T14:16:55.137Z
Comments.Text: This could be a duplicate question as @acvill is indicating
Comments.UserDisplayName: M__
Tags: <sam><pacbio>
Title: Under what circumstances can the SEQ field in a SAM file be a *?
ThreadText: # Under what circumstances can the SEQ field in a SAM file be a *?
  
  (Asked by: username_0 on 2022-02-03)
  
  I saw in the SAM format specifications that the SEQ field (10th column) can be a "\*" if the sequence is not stored, instead of being the sequence of the mapped read. Under what circumstances is this expected to occur? I don't understand why it's allowed in the spec.
  
  For a concrete example, I have pacbio data mapped to a reference sequence, and some of the records in the SAM file have a sequence of \*, and I don't know why or if that means anything. I don't understand why they exist, since the data is ostensibly present in the FASTQ file I use as input to the read mapper, and I don't understand what purpose they could have, since it seems to me that these records couldn't be interpreted by variant calling software. At best it would seem they can be used to infer coverage, but it's coverage by sequences of an uncertain nature?
  
  **Tags:** sam, pacbio
  
  > **Comments:**
  > **username_1**: Related: [How to output all sequences with bwa mem, not `*`?](https://bioinformatics.stackexchange.com/q/5579/3967)  
  > **username_0**: Sounds like I should check if these are exclusively secondary alignments  
  > **username_2**: This could be a duplicate question as @username_1 is indicating  
  
  ---
  
  ## 0 answers
  
  