Samtools is a suite of programs for interacting with high-throughput sequencing data.
The Samtools module parses results generated by Samtools, a suite of programs for interacting with high-throughput sequencing data.
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,
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 shared: true samtools/flagstat: contents: in total (QC-passed reads + QC-failed reads) shared: true samtools/idxstats: fn: "*idxstat*" samtools/rmdup: contents: "[bam_rmdup" shared: true