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---
name: Bamdst
url: https://github.com/shiquan/bamdst
description: >
Bamdst is a lightweight tool to stat the depth coverage of target regions of bam file(s).
---
The MultiQC module reads data from two types of Bamdst logs:
- `coverage.report`: used to build a table with coverage statistics. The sample name is read from this file.
- `chromosomes.report`: if this file is found in the same directory as the file above, additionally a per-contig coverage plot will be generated.
Note that for the sample names, the module will attempt to use the input BAM name
in the header in the `coverage.report` file:
```
## The file was created by bamdst
## Version : 1.0.9
## Files : ST0217_Lg.bam
...
```
However, if the tool was run in a piped manner, the file name will be just `-` or `/dev/stdin`,
and instead MultiQC will fall back to using the log file name `coverage.report`.
Make sure to run MultiQC with `--dirs` if use have multiple samples run in this way,
otherwise MultiQC will only report the first found sample under the name `coverage`.
For the per-contig coverage plot, you can include and exclude contigs based on name or pattern.
For example, you could add the following to your MultiQC config file:
```yaml
bamdst:
include_contigs:
- "chr*"
exclude_contigs:
- "*_alt"
- "*_decoy"
- "*_random"
- "*_fix"
- "HLA*"
- "chrUn*"
- "chrEBV"
- "chrM"
```
Note that exclusion supersedes inclusion for the contig filters.
To additionally avoid cluttering the plot, MultiQC can exclude contigs with a low relative coverage.
```yaml
bamdst:
# Should be a fraction, e.g. 0.001 (exclude contigs with 0.1% coverage of sum of
# coverages across all contigs)
perchrom_fraction_cutoff: 0.001
```
If you want to see what is being excluded, you can set `show_excluded_debug_logs` to `True`:
```yaml
bamdst:
show_excluded_debug_logs: True
```
This will then print a debug log message (use `multiqc -v`) for each excluded contig.
This is disabled by default as there can be very many in some cases.
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