Samtools mpileup

Generate VCF, BCF or pileup for BAM file(s).

Software dependencies

• samtools >=1.6

Example

rule samtools_mpileup:
  input:
    "{sample}.bam" # One or many sam/bam/cram file(s)
  output:
    "{sample}.mpileup" # A pileup file
  params:
    options: "" # Additional command line options
  wrapper:
    "samtools/mpileup"

Usage

Run snakemake with

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

to automatically download the wrapper samtools/mpileup 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

• Jens Preussner