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: https://github.com/bwa-mem2/bwa-mem2

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:
        "v1.15.2/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.

Notes

• The extra param allows for additional arguments for bwa-mem2.
• The sorting param allows to enable sorting, and can be either ‘none’, ‘samtools’ or ‘picard’.
• The sort_extra allows for extra arguments for samtools/picard

Software dependencies

• bwa-mem2=2.2
• samtools=1.15
• picard-slim=2.27
• snakemake-wrapper-utils=0.5

Input/Output

Input:

• FASTQ file(s)
• reference genome

Output:

• SAM/BAM/CRAM file

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"


import tempfile
from os import path
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
from snakemake_wrapper_utils.samtools import get_samtools_opts


# Extract arguments.
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=False, stderr=True)
sort = snakemake.params.get("sort", "none")
sort_order = snakemake.params.get("sort_order", "coordinate")
sort_extra = snakemake.params.get("sort_extra", "")
samtools_opts = get_samtools_opts(snakemake)
java_opts = get_java_opts(snakemake)


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]


# 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(f"Unexpected value for sort_order ({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 {samtools_opts}"

elif sort == "samtools":
    # Sort alignments using samtools sort.
    pipe_cmd = "samtools sort {samtools_opts} {sort_extra} -T {tmpdir}"

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

elif sort == "picard":
    # Sort alignments using picard SortSam.
    pipe_cmd = "picard SortSam {java_opts} {sort_extra} --INPUT /dev/stdin --TMP_DIR {tmpdir} --SORT_ORDER {sort_order} --OUTPUT {snakemake.output[0]}"

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


with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "(bwa-mem2 mem"
        " -t {snakemake.threads}"
        " {extra}"
        " {index}"
        " {snakemake.input.reads}"
        " | " + pipe_cmd + ") {log}"
    )