SAMTOOLS FLAGSTAT
Use samtools to create a flagstat file from a bam or sam file.
Example
This wrapper can be used in the following way:
rule samtools_flagstat:
input:
"mapped/{sample}.bam",
output:
"mapped/{sample}.bam.flagstat",
log:
"{sample}.log",
params:
extra="", # optional params string
wrapper:
"v5.7.0/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.
Notes
The extra param allows for additional program arguments (not -@/–threads).
For more information see, http://www.htslib.org/doc/samtools-flagstat.html
Software dependencies
samtools=1.21
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
bam or sam file (.bam,.sam)
Output:
flagstat file (.flagstat)
Code
__author__ = "Christopher Preusch"
__copyright__ = "Copyright 2017, Christopher Preusch"
__email__ = "cpreusch[at]ust.hk"
__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", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
"samtools flagstat {samtools_opts} {extra} {snakemake.input[0]} > {snakemake.output[0]} {log}"
)