Samtools index¶

Index bam file with samtools.

Software dependencies¶

rule samtools_index:
  input:
    bam file
  output:
    bam file index (.bai)
  wrapper:
    "samtools/index"

Run snakemake with

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

to automatically download the wrapper samtools/index 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.