Samtools view¶
Convert or filter SAM/BAM.
Software dependencies¶
- samtools ==1.6
Example¶
rule samtools_view:
input:
"{sample}.sam"
output:
"{sample}.bam"
params:
"-b"
wrapper:
"samtools/view"
Usage¶
Run snakemake with
snakemake --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/
to automatically download the wrapper samtools/view
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