Samtools flagstat

Use samtools to create a flagstat file from a bam or sam file.

Software dependencies

• samtools ==1.6

Example

rule samtools_flagstat:
  input:
    "mapped/{sample}.bam" # bam or sam file (.bam,.sam)
  output:
    "stat/{sample}.txt" # flagstat file (.flagstat)
  wrapper:
    "samtools/flagstat"

Usage

Run snakemake with

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

to automatically download the wrapper samtools/flagstat 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

• Christopher Preusch