Samtools sort

Sort bam file with samtools.

Software dependencies

• samtools ==1.6

Example

rule samtools_sort:
  input:
    "{sample}.bam" # A sam/bam/cram file
  output:
    "{sample}_sorted.bam" # A sorted sam/bam/cram file
  wrapper:
    "samtools/sort"

Usage

Run snakemake with

snakemake --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/

to automatically download the wrapper samtools/sort and include it in the snakefile.

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