BWA MEM

Map reads using bwa mem, with optional sorting using samtools or picard. For more information about BWA see BWA documentation.

Example

This wrapper can be used in the following way:

rule bwa_mem:
    input:
        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"]
    output:
        "mapped/{sample}.bam"
    log:
        "logs/bwa_mem/{sample}.log"
    params:
        index="genome",
        extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
        sort="none",             # Can be 'none', 'samtools' or 'picard'.
        sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
        sort_extra=""            # Extra args for samtools/picard.
    threads: 8
    wrapper:
        "0.75.0/bio/bwa/mem"

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

• bwa==0.7.17
• samtools==1.12
• picard==2.20.1

Authors

• Johannes Köster
• Julian de Ruiter

Code

__author__ = "Johannes Köster, Julian de Ruiter"
__copyright__ = "Copyright 2016, Johannes Köster and Julian de Ruiter"
__email__ = "koester@jimmy.harvard.edu, julianderuiter@gmail.com"
__license__ = "MIT"


from os import path

from snakemake.shell import shell


# Extract arguments.
extra = snakemake.params.get("extra", "")

sort = snakemake.params.get("sort", "none")
sort_order = snakemake.params.get("sort_order", "coordinate")
sort_extra = snakemake.params.get("sort_extra", "")

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

# Check inputs/arguments.
if not isinstance(snakemake.input.reads, str) and len(snakemake.input.reads) not in {
    1,
    2,
}:
    raise ValueError("input must have 1 (single-end) or " "2 (paired-end) elements")

if sort_order not in {"coordinate", "queryname"}:
    raise ValueError("Unexpected value for sort_order ({})".format(sort_order))

# Determine which pipe command to use for converting to bam or sorting.
if sort == "none":

    # Simply convert to bam using samtools view.
    pipe_cmd = "samtools view -Sbh -o {snakemake.output[0]} -"

elif sort == "samtools":

    # Sort alignments using samtools sort.
    pipe_cmd = "samtools sort {sort_extra} -o {snakemake.output[0]} -"

    # Add name flag if needed.
    if sort_order == "queryname":
        sort_extra += " -n"

    prefix = path.splitext(snakemake.output[0])[0]
    sort_extra += " -T " + prefix + ".tmp"

elif sort == "picard":

    # Sort alignments using picard SortSam.
    pipe_cmd = (
        "picard SortSam {sort_extra} INPUT=/dev/stdin"
        " OUTPUT={snakemake.output[0]} SORT_ORDER={sort_order}"
    )

else:
    raise ValueError("Unexpected value for params.sort ({})".format(sort))

shell(
    "(bwa mem"
    " -t {snakemake.threads}"
    " {extra}"
    " {snakemake.params.index}"
    " {snakemake.input.reads}"
    " | " + pipe_cmd + ") {log}"
)