BCFTOOLS STATS¶
Generate VCF stats using bcftools stats.
URL: https://github.com/samtools/bcftools
Example¶
This wrapper can be used in the following way:
rule bcf_stats:
input:
"{prefix}"
output:
"{prefix}.stats.txt"
log:
"{prefix}.bcftools.stats.log"
params:
""
wrapper:
"v1.3.2/bio/bcftools/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¶
bcftools==1.12
Authors¶
- William Rowell
Code¶
__author__ = "William Rowell"
__copyright__ = "Copyright 2020, William Rowell"
__email__ = "wrowell@pacb.com"
__license__ = "MIT"
from snakemake.shell import shell
# bcftools takes additional decompression threads through --threads
# Other threads are *additional* threads passed to the '--threads' argument
threads = (
"" if snakemake.threads <= 1 else " --threads {} ".format(snakemake.threads - 1)
)
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
shell(
"bcftools stats {threads} {snakemake.params} {snakemake.input} > {snakemake.output} {log}"
)