BAMTOOLS STATS

Use bamtools to collect statistics from a BAM file. For more information about bamtools see bamtools documentation and bamtools source code.

URL: https://github.com/pezmaster31/bamtools

Example

This wrapper can be used in the following way:

rule bamtools_stats:
    input:
        "{sample}.bam"
    output:
        "{sample}.bamstats"
    params:
        "-insert" # optional summarize insert size data
    log:
        "logs/bamtools/stats/{sample}.log"
    wrapper:
        "v1.9.0/bio/bamtools/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.

Notes

A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf This tool/wrapper does not handle multi threading

Software dependencies

• bamtools==2.5.1

Input/Output

Input:

• bam files (.bam), must be in first position

Output:

• bamstats file (.bamstats), must be in first position

Params

• Optional parameters as first and only value.:

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(
    "(bamtools stats {snakemake.params} -in {snakemake.input[0]} > {snakemake.output[0]}) {log}"
)