Samtools

Description

The Samtools module parses results generated by Samtools, a suite of programs for interacting with high-throughput sequencing data.

Supported commands:

• stats
• flagstats
• idxstats
• rmdup
• coverage
• markdup

idxstats

The samtools idxstats prints its results to standard out (no consistent file name) and has no header lines (no way to recognise from content of file). As such, idxstats result files must have the string idxstat somewhere in the filename.

There are a few MultiQC config options that you can add to customise how the idxstats module works. A typical configuration could look as follows:

# Always include these chromosomes in the plot
samtools_idxstats_always:
  - X
  - Y
 
# Never include these chromosomes in the plot
samtools_idxstats_ignore:
  - MT
 
# Threshold where chromosomes are ignored in the plot.
# Should be a fraction, default is 0.001 (0.1% of total)
samtools_idxstats_fraction_cutoff: 0.001
 
# Name of the X and Y chromosomes.
# If not specified, MultiQC will search for any chromosome
# names that look like x, y, chrx or chry (case insensitive search)
samtools_idxstats_xchr: myXchr
samtools_idxstats_ychr: myYchr

File search patterns

samtools/stats:
  contents: This file was produced by samtools stats
samtools/flagstat:
  contents: in total (QC-passed reads + QC-failed reads)
samtools/idxstats:
  fn: "*idxstat*"
samtools/rmdup:
  contents: "[bam_rmdup"
samtools/coverage:
  contents: "#rname\tstartpos\tendpos\tnumreads\tcovbases\tcoverage\tmeandepth\tm\
    eanbaseq\tmeanmapq"
  num_lines: 10
samtools/markdup_txt:
  contents: "COMMAND: samtools markdup"
  num_lines: 2
samtools/markdup_json:
  contents: '"COMMAND": "samtools markdup'
  num_lines: 10