Bamdst

note

Lightweight tool to stat the depth coverage of target regions of BAM file(s).

https://https://github.com/shiquan/bamdst

The 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. This file must be named exactly this way, with the .report extension.

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:

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.

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:

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.

File search patterns

bamdst/coverage:
  contents: '## The file was created by bamdst'
  num_lines: 5