Answers.Body: <p>The documentation on the GitHub page you linked to <a href="https://github.com/Illumina/manta/tree/master/docs/userGuide#generating-evidence-bams" rel="nofollow noreferrer">has this to say</a> about the <code>evidence</code> folder:</p>
  <blockquote>
  <p><strong>Generating evidence bams</strong></p>
  <p>Using the <code>--generateEvidenceBam</code> option, Manta can be configured to
  generate bam files of evidence reads for SVs listed in the candidate
  vcf file.</p>
  <p>It is recommended to use this option together with the --region
  option, so that the analysis is limited to relatively small genomic
  regions for debugging purposes.</p>
  <p>The evidence bam files are provided in
  <code>${MANTA_ANALYSIS_PATH}/results/evidence</code>, with a naming format
  <code>evidence_*.*.bam</code>. There is one such file for each input bam of the
  analysis, containing evidence reads of the candidate SVs identified
  from that input bam. Each read in an evidence bam keeps all
  information from the original bam, and it contains also a customized
  tag in the format:
  <code>ZM:Z:${MANTA_SV_ID_1}|${EVIDENCE_TYPE},${MANTA_SV_ID_2}|${EVIDENCE_TYPE}</code>.
  For example, <code>ZM:Z:MantaINV:5:0:1:0:0:0|PR|SRM,MantaDEL:5:1:2:0:0:0|SR</code></p>
  <p>One read can have more than one of the three evidence types: PR for
  paired reads, SR for split reads, and SRM for split read mates. One
  read can be evidence for multiple SVs, which are separated by commas
  in the tag. Notice that the number of evidence reads for a particular
  SV in the evidence bam files could be more than the evidence counts
  (PR and SR) in the final vcf files. This is because more stringent
  criteria are applied for generating evidence counts in the final vcf
  files.</p>
  </blockquote>
  <p>So it looks to me like you need the <code>--generateEvidenceBam</code> option to generate evidence, but that the directory <code>evidence</code> is created regardless of whether you use the option. Try running the analysis again, but using <code>--generateEvidenceBam</code> this time.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-04-24T12:47:44.267Z
Answers.Text: Thank you I checked the documentation again this seems to be the case. It is just an empty folder until `--generateEvidenceBam` is specified.
Answers.UserDisplayName: Indira
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-04-19T09:02:03.493Z
Answers.LastActivityDate: 2023-04-19T09:02:03.493Z
Answers.UserDisplayName: terdon
Body: <p>I am looking at <a href="https://github.com/Illumina/manta/tree/master/docs/userGuide" rel="nofollow noreferrer">Manta on Github</a> and I ran a bit of code:</p>
  <p>The following variables were defined in the code:</p>
  <ul>
  <li><code>input_dir</code> is the file path to a folder with less than 10 .bams as per the limitations of Manta</li>
  <li><code>output_dir</code> is the path to the output</li>
  <li><code>MANTA_INSTALL_PATH</code> is the path to the Manta installation</li>
  <li><code>reference</code> is the path to the reference fasta</li>
  </ul>
  <pre><code>    for file in <span class="math-container">${input_dir}/*.bam
  do
    # Create subdirectory named after bam file
    sub_dir=$</span>{output_dir}/<span class="math-container">$(basename $</span>{file} .bam)
        mkdir -p ${sub_dir}
      
        # Use reference fasta path specified by user
        <span class="math-container">${MANTA_INSTALL_PATH}/bin/configManta.py \
      --bam $</span>file \
          --referenceFasta <span class="math-container">${reference} \
      --runDir $</span>{sub_dir} \
          --exome
      done
  
  # Now run each `runWorkflow.py`
  
  find &quot;$output_dir&quot; -name &quot;runWorkflow.py&quot; -exec {} \;
  
  </code></pre>
  <p>The run worked and each sample had a folder with the following files:</p>
  <pre><code>results  runWorkflow.py  runWorkflow.py.config.pickle  workflow.error.log.txt  workflow.exitcode.txt  workflow.warning.log.txt  workspace
  </code></pre>
  <p>Each <code>workflow.error.log.txt</code> had nothing in it implying the the run had been successful. Each <code>results</code> folder had 3 subfolders</p>
  <pre><code>evidence  stats  variants
  </code></pre>
  <p>The <code>stats</code> and <code>variants</code> folder each had outputs but the <code>evidence</code> folder had nothing. Is this normal? Should it have something in this folder? Why is this folder there in Manta if nothing is in it?</p>
  
Tags: <git>
Title: Manta Evidence Folder Is Empty
ThreadText: # Manta Evidence Folder Is Empty
  
  (Asked by: username_0 on 2023-04-17)
  
  I am looking at [Manta on Github](https://github.com/Illumina/manta/tree/master/docs/userGuide) and I ran a bit of code:
  
  The following variables were defined in the code:
  
  * `input_dir` is the file path to a folder with less than 10 .bams as per the limitations of Manta
  * `output_dir` is the path to the output
  * `MANTA_INSTALL_PATH` is the path to the Manta installation
  * `reference` is the path to the reference fasta
  
  ```
      for file in ${input_dir}/*.bam
  do
    # Create subdirectory named after bam file
    sub_dir=${output_dir}/$(basename ${file} .bam)
        mkdir -p ${sub_dir}
      
        # Use reference fasta path specified by user
        ${MANTA_INSTALL_PATH}/bin/configManta.py \
      --bam $file \
          --referenceFasta ${reference} \
      --runDir ${sub_dir} \
          --exome
      done
  
  # Now run each `runWorkflow.py`
  
  find "$output_dir" -name "runWorkflow.py" -exec {} \;
  
  ```
  
  The run worked and each sample had a folder with the following files:
  
  ```
  results  runWorkflow.py  runWorkflow.py.config.pickle  workflow.error.log.txt  workflow.exitcode.txt  workflow.warning.log.txt  workspace
  
  ```
  
  Each `workflow.error.log.txt` had nothing in it implying the the run had been successful. Each `results` folder had 3 subfolders
  
  ```
  evidence  stats  variants
  
  ```
  
  The `stats` and `variants` folder each had outputs but the `evidence` folder had nothing. Is this normal? Should it have something in this folder? Why is this folder there in Manta if nothing is in it?
  
  **Tags:** git
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-04-19. Score: 1 | Accepted answer
  
  The documentation on the GitHub page you linked to [has this to say](https://github.com/Illumina/manta/tree/master/docs/userGuide#generating-evidence-bams) about the `evidence` folder:
  
  > **Generating evidence bams**
  >
  > Using the `--generateEvidenceBam` option, Manta can be configured to
  > generate bam files of evidence reads for SVs listed in the candidate
  > vcf file.
  >
  > It is recommended to use this option together with the --region
  > option, so that the analysis is limited to relatively small genomic
  > regions for debugging purposes.
  >
  > The evidence bam files are provided in
  > `${MANTA_ANALYSIS_PATH}/results/evidence`, with a naming format
  > `evidence_*.*.bam`. There is one such file for each input bam of the
  > analysis, containing evidence reads of the candidate SVs identified
  > from that input bam. Each read in an evidence bam keeps all
  > information from the original bam, and it contains also a customized
  > tag in the format:
  > `ZM:Z:${MANTA_SV_ID_1}|${EVIDENCE_TYPE},${MANTA_SV_ID_2}|${EVIDENCE_TYPE}`.
  > For example, `ZM:Z:MantaINV:5:0:1:0:0:0|PR|SRM,MantaDEL:5:1:2:0:0:0|SR`
  >
  > One read can have more than one of the three evidence types: PR for
  > paired reads, SR for split reads, and SRM for split read mates. One
  > read can be evidence for multiple SVs, which are separated by commas
  > in the tag. Notice that the number of evidence reads for a particular
  > SV in the evidence bam files could be more than the evidence counts
  > (PR and SR) in the final vcf files. This is because more stringent
  > criteria are applied for generating evidence counts in the final vcf
  > files.
  
  So it looks to me like you need the `--generateEvidenceBam` option to generate evidence, but that the directory `evidence` is created regardless of whether you use the option. Try running the analysis again, but using `--generateEvidenceBam` this time.
  
  > **Comments:**
  > **username_0**: Thank you I checked the documentation again this seems to be the case. It is just an empty folder until `--generateEvidenceBam` is specified.  
  
  ---
  
  