SAMTOOLS STATS¶
Generate stats using samtools.
URL:
Example¶
This wrapper can be used in the following way:
rule samtools_stats:
input:
"mapped/{sample}.bam",
output:
"samtools_stats/{sample}.txt",
params:
extra="", # Optional: extra arguments.
region="xx:1000000-2000000", # Optional: region string.
log:
"logs/samtools_stats/{sample}.log",
wrapper:
"v1.2.0/bio/samtools/stats"
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=1.14
snakemake-wrapper-utils=0.3
Notes¶
- The extra param allows for additional program arguments (not -@/–threads).
- For more information see, http://www.htslib.org/doc/samtools-stats.html
Authors¶
- Julian de Ruiter
- Filipe G. Vieira
Code¶
"""Snakemake wrapper for trimming paired-end reads using cutadapt."""
__author__ = "Julian de Ruiter"
__copyright__ = "Copyright 2017, Julian de Ruiter"
__email__ = "julianderuiter@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.samtools import get_samtools_opts
samtools_opts = get_samtools_opts(
snakemake, parse_write_index=False, parse_output=False, parse_output_format=False
)
extra = snakemake.params.get("extra", "")
region = snakemake.params.get("region", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
"samtools stats {samtools_opts} {extra} {snakemake.input} {region} > {snakemake.output} {log}"
)