SAMTOOLS INDEX
Index bam file with samtools.
Example
This wrapper can be used in the following way:
rule samtools_index:
input:
"mapped/{sample}.sorted.bam",
output:
"mapped/{sample}.sorted.bam.bai",
log:
"logs/samtools_index/{sample}.log",
params:
extra="", # optional params string
threads: 4 # This value - 1 will be sent to -@
wrapper:
"v5.8.0-3-g915ba34/bio/samtools/index"
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.
For more information see, http://www.htslib.org/doc/samtools-index.html
Software dependencies
samtools=1.21
Input/Output
Input:
bam file
Output:
bam file index (.bai)
Code
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
# Samtools takes additional threads through its option -@
# One thread for samtools merge
# Other threads are *additional* threads passed to the '-@' argument
threads = "" if snakemake.threads <= 1 else " -@ {} ".format(snakemake.threads - 1)
shell(
"samtools index {threads} {extra} {snakemake.input[0]} {snakemake.output[0]} {log}"
)