SAMTOOLS INDEX

Index bam file with samtools.

Software dependencies

  • samtools ==1.5

Example

This wrapper can be used in the following way:

rule samtools_index:
    input:
        "A.sorted.bam"
    output:
        "A.sorted.bam.bai"
    params:
        "" # optional params string
    wrapper:
        "0.18.0/bio/samtools/index"

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

  • Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell("samtools index {snakemake.params} {snakemake.input[0]} {snakemake.output[0]}")