<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>

CC BY-SA 4.0
2023-04-24T12:47:44.267Z
Thank you I checked the documentation again this seems to be the case. It is just an empty folder until `--generateEvidenceBam` is specified.
Indira
CC BY-SA 4.0
2023-04-19T09:02:03.493Z
2023-04-19T09:02:03.493Z
terdon
<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>

<git>
Manta Evidence Folder Is Empty
# Manta Evidence Folder Is Empty

(Asked by: username_0 on 2023-04-17)

I am looking at Manta on Github 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.  

---

