SAMTOOLS IDXSTATS

Use samtools to retrieve and print stats form indexed bam, sam or cram files

Software dependencies

  • samtools ==1.10

Example

This wrapper can be used in the following way:

rule samtools_idxstats:
    input:
        bam="mapped/{sample}.bam",
        idx="mapped/{sample}.bam.bai"
    output:
        "mapped/{sample}.bam.idxstats"
    log:
        "logs/samtools/idxstats/{sample}.log"
    wrapper:
        "0.65.0/bio/samtools/idxstats"

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

  • Antonie Vietor

Code

__author__ = "Antonie Vietor"
__copyright__ = "Copyright 2020, Antonie Vietor"
__email__ = "antonie.v@gmx.de"
__license__ = "MIT"


from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

shell("samtools idxstats {snakemake.input.bam} > {snakemake.output[0]} {log}")