Answers.Body: <p>This is how I do it.</p>
  <pre><code>samtools view -@5 -f 0x800 -hb /path/sample.bam &gt; sup.bam
  </code></pre>
  <p>Then if you want it as a fasta</p>
  <pre><code>samtools view -F 0x1 -hb sup.bam | samtools fasta -F 0x1 - &gt; sup.fa
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-18T05:52:23.110Z
Answers.Text: Thanks !! It works great. I will use samtools source code to write a small program to extract the reads based on flag.
Answers.UserDisplayName: SBDK8219
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-18T07:02:18.523Z
Answers.Text: Pysam wraps it pretty well, just fyi
Answers.UserDisplayName: Liam McIntyre
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-02-17T10:45:38.887Z
Answers.LastActivityDate: 2021-02-17T10:45:38.887Z
Answers.UserDisplayName: Liam McIntyre
Body: <p>I am trying to extract all chimeric and multi-map reads from either SAM/BAM file. Is there any simple command to do that? Can I use <code>htslib</code> for parsing sam/bam files and extracting based on any flags. Any help on how to start will be appreciated.</p>
  
Tags: <sam><htslib>
Title: extract chimeric and multimap reads from bam file
ThreadText: # extract chimeric and multimap reads from bam file
  
  (Asked by: username_0 on 2021-02-17)
  
  I am trying to extract all chimeric and multi-map reads from either SAM/BAM file. Is there any simple command to do that? Can I use `htslib` for parsing sam/bam files and extracting based on any flags. Any help on how to start will be appreciated.
  
  **Tags:** sam, htslib
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-02-17. Score: 1
  
  This is how I do it.
  
  ```
  samtools view -@5 -f 0x800 -hb /path/sample.bam > sup.bam
  
  ```
  
  Then if you want it as a fasta
  
  ```
  samtools view -F 0x1 -hb sup.bam | samtools fasta -F 0x1 - > sup.fa
  
  ```
  
  > **Comments:**
  > **username_0**: Thanks !! It works great. I will use samtools source code to write a small program to extract the reads based on flag.  
  > **username_1**: Pysam wraps it pretty well, just fyi  
  
  ---
  
  