BWA-MEM2

Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Optional sorting using samtools or picard.

URL:

Example

This wrapper can be used in the following way:

rule bwa_mem2_mem:
    input:
        reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
        # Index can be a list of (all) files created by bwa, or one of them
        idx=multiext("genome.fasta", ".amb", ".ann", ".bwt.2bit.64", ".pac"),
    output:
        "mapped/{sample}.bam",
    log:
        "logs/bwa_mem2/{sample}.log",
    params:
        extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
        sort="none",  # Can be 'none', 'samtools' or 'picard'.
        sort_order="coordinate",  # Can be 'coordinate' (default) or 'queryname'.
        sort_extra="",  # Extra args for samtools/picard.
    threads: 8
    wrapper:
        "v1.2.1/bio/bwa-mem2/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-mem2==2.2.1
• samtools==1.12
• picard==2.23

Authors

• Christopher Schröder
• Johannes Köster
• Julian de Ruiter

Code

__author__ = "Christopher Schröder, Johannes Köster, Julian de Ruiter"
__copyright__ = (
    "Copyright 2020, Christopher Schröder, Johannes Köster and Julian de Ruiter"
)
__email__ = "christopher.schroeder@tu-dortmund.de 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", "")

index = snakemake.input.get("index", "")
if isinstance(index, str):
    index = path.splitext(snakemake.input.idx)[0]
else:
    index = path.splitext(snakemake.input.idx[0])[0]

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-mem2 mem"
    " -t {snakemake.threads}"
    " {extra}"
    " {index}"
    " {snakemake.input.reads}"
    " | " + pipe_cmd + ") {log}"
)