SAMTOOLS STATS

Generate stats using samtools.

Software dependencies

  • samtools ==1.5

Example

This wrapper can be used in the following way:

rule samtools_stats:
    input:
        "mapped/{sample}.bam"
    output:
        "samtools_stats/{sample}.txt"
    params:
        extra="",                       # Optional: extra arguments.
        region="1:1000000-2000000"      # Optional: region string.
    log:
        "logs/samtools_stats/{sample}.log"
    wrapper:
        "0.19.4/bio/samtools/stats"

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

Code

"""Snakemake wrapper for trimming paired-end reads using cutadapt."""

__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell


extra = snakemake.params.get("extra", "")
region = snakemake.params.get("region", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)


shell("samtools stats {extra} {snakemake.input}"
      " {region} > {snakemake.output} {log}")