SAMTOOLS FLAGSTAT¶
Use samtools to create a flagstat file from a bam or sam file. For more information see SAMtools documentation.
Example¶
This wrapper can be used in the following way:
rule samtools_flagstat:
input:
"mapped/{sample}.bam"
output:
"mapped/{sample}.bam.flagstat"
wrapper:
"0.71.0/bio/samtools/flagstat"
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.
Software dependencies¶
samtools==1.10
Authors¶
- Christopher Preusch
Code¶
__author__ = "Christopher Preusch"
__copyright__ = "Copyright 2017, Christopher Preusch"
__email__ = "cpreusch[at]ust.hk"
__license__ = "MIT"
from snakemake.shell import shell
shell("samtools flagstat {snakemake.input[0]} > {snakemake.output[0]}")