BCFTOOLS CALL¶
Call variants with bcftools call.
URL:
Example¶
This wrapper can be used in the following way:
rule bcftools_call:
input:
pileup="{sample}.pileup.bcf",
output:
calls="{sample}.calls.bcf",
params:
caller="-m", # valid options include -c/--consensus-caller or -m/--multiallelic-caller
options="--ploidy 1 --prior 0.001",
log:
"logs/bcftools_call/{sample}.log",
wrapper:
"0.85.0/bio/bcftools/call"
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=1.11
Authors¶
- Johannes Köster
- Michael Hall
Code¶
__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"
from snakemake.shell import shell
class CallerOptionError(Exception):
pass
valid_caller_opts = {"-c", "--consensus-caller", "-m", "--multiallelic-caller"}
caller_opt = snakemake.params.get("caller", "")
if caller_opt.strip() not in valid_caller_opts:
raise CallerOptionError(
"bcftools call expects either -m/--multiallelic-caller or "
"-c/--consensus-caller as caller option."
)
options = snakemake.params.get("options", "")
shell(
"bcftools call {options} {caller_opt} --threads {snakemake.threads} "
"-o {snakemake.output.calls} {snakemake.input.pileup} 2> {snakemake.log}"
)