BCFTOOLS MPILEUP

Generate VCF or BCF containing genotype likelihoods for one or multiple alignment (BAM or CRAM) files with bcftools mpileup.

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:
        "v1.6.0/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}"
)