BCFTOOLS MPILEUP¶
Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files with bcftools mpileup.
URL:
Example¶
This wrapper can be used in the following way:
rule bcftools_mpileup:
input:
index="genome.fasta.fai",
ref="genome.fasta", # this can be left out if --no-reference is in options
alignments="mapped/{sample}.bam",
output:
pileup="pileups/{sample}.pileup.bcf",
params:
options="--max-depth 100 --min-BQ 15",
log:
"logs/bcftools_mpileup/{sample}.log",
wrapper:
"v1.1.0/bio/bcftools/mpileup"
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¶
- Michael Hall
Code¶
__author__ = "Michael Hall"
__copyright__ = "Copyright 2020, Michael Hall"
__email__ = "michael@mbh.sh"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
class MissingReferenceError(Exception):
pass
options = snakemake.params.get("options", "")
# determine if a fasta reference is provided or not and add to options
if "--no-reference" not in options:
ref = snakemake.input.get("ref", "")
if not ref:
raise MissingReferenceError(
"The --no-reference option was not given, but no fasta reference was "
"provided."
)
options += " --fasta-ref {}".format(ref)
shell(
"bcftools mpileup {options} --threads {snakemake.threads} "
"--output {snakemake.output.pileup} "
"{snakemake.input.alignments} "
"{log}"
)