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---
name: Samtools
url: http://www.htslib.org
description: >
Samtools is a suite of programs for interacting with high-throughput
sequencing data.
---
The Samtools module parses results generated by
[Samtools](http://www.htslib.org),
a suite of programs for interacting with high-throughput
sequencing data.
Supported commands:
- `stats`
- `flagstats`
- `idxstats`
- `rmdup`
### 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:
```yaml
# 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
```
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