SAMTOOLS IDXSTATS

Use samtools to retrieve and print stats form indexed bam, sam or cram files. For more information see SAMtools documentation.

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:
        "0.68.0/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.

Software dependencies

• samtools==1.10

Input/Output

Input:

• indexed sam, bam or cram file (.sam, .bam, .cram)
• corresponding index files

Output:

• idxstat file (.idxstats)

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}")