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}"
)