Body: <p>I want to export the list of soft-clipped regions into a csv file from a region of interest in IGV. Additional information regarding the soft-clipped sequence, coordinate and nucleotide length will be helpful.
  <a href="https://i.sstatic.net/2lM8V.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/2lM8V.png" alt="enter image description here" /></a></p>
  <p>PFB the output file format</p>
  <div class="s-table-container">
  <table class="s-table">
  <thead>
  <tr>
  <th>Gene</th>
  <th>Variant</th>
  </tr>
  </thead>
  <tbody>
  <tr>
  <td>FLT3</td>
  <td>chr13:28034082C&gt;CAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATAG</td>
  </tr>
  <tr>
  <td>FLT3</td>
  <td>chr13:28034113T&gt;TTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCACC</td>
  </tr>
  </tbody>
  </table>
  </div>
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-02T11:06:37.543Z
Comments.Text: Does this have to be done from IGV?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-05-02T13:09:49.760Z
Comments.Text: Also, please [edit] your question and add an example of the output format you want to see. What _exact_ fields should be in the csv?
Comments.UserDisplayName: terdon
Tags: <sam><igv>
Title: How to export the list of soft-clipped regions from a region of interest in IGV
ThreadText: # How to export the list of soft-clipped regions from a region of interest in IGV
  
  (Asked by: username_0 on 2023-05-02)
  
  I want to export the list of soft-clipped regions into a csv file from a region of interest in IGV. Additional information regarding the soft-clipped sequence, coordinate and nucleotide length will be helpful.
  [![enter image description here](https://i.sstatic.net/2lM8V.png)](https://i.sstatic.net/2lM8V.png)
  
  PFB the output file format
  
  | Gene | Variant |
  | --- | --- |
  | FLT3 | chr13:28034082C>CAAACTCTAAATTTTCTCTTGGAAACTCCCATTTGAGATCATATAG |
  | FLT3 | chr13:28034113T>TTTGAGATCATATTCATATTCTCTGAAATCAACGTAGAAGTACTCATTATCTGAGGAGCCGGTCACCTGTACCACC |
  
  **Tags:** sam, igv
  
  > **Comments:**
  > **username_1**: Does this have to be done from IGV?  
  > **username_1**: Also, please [edit] your question and add an example of the output format you want to see. What _exact_ fields should be in the csv?  
  
  ---
  
  ## 0 answers
  
  