Samtools stats

Generate stats using samtools.

Software dependencies

• samtools ==1.6

Example

rule samtools_stats:
  input:
    "{sample}.bam"
  output:
    "{sample}.stats.txt"
  params:
    region = "",
    extra = "" # Additional parameters
  wrapper:
    "samtools/stats"

Usage

Run snakemake with

snakemake --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/

to automatically download the wrapper samtools/stats and include it in the snakefile.

Note that input, output and log file paths can be chosen freely. When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Authors

• Julian de Ruiter