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Bamdst

Supported Tool

Bamdst is a lightweight tool to stat the depth coverage of target regions of bam file(s).

Description

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:

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