BAZAM

Bazam is a smarter way to realign reads from one genome to another. If you’ve tried to use Picard SAMtoFASTQ or samtools bam2fq before and ended up unsatisfied with complicated, long running inefficient pipelines, bazam might be what you wanted. Bazam will output FASTQ in a form that can stream directly into common aligners such as BWA or Bowtie2, so that you can quickly and easily realign reads without extraction to any intermediate format. Bazam can target a specific region of the genome, specified as a region or a gene name if you prefer.

URL: https://github.com/ssadedin/bazam

Example

This wrapper can be used in the following way:

rule bazam_interleaved:
    input:
        bam="mapped/{sample}.bam",
        bai="mapped/{sample}.bam.bai",
    output:
        reads="results/reads/{sample}.fastq.gz",
    resources:
        mem_mb=12000,
    log:
        "logs/bazam/{sample}.log",
    wrapper:
        "v1.17.2/bio/bazam"


rule bazam_separated:
    input:
        bam="mapped/{sample}.cram",
        bai="mapped/{sample}.cram.crai",
        reference="genome.fasta",
    output:
        r1="results/reads/{sample}.r1.fastq.gz",
        r2="results/reads/{sample}.r2.fastq.gz",
    resources:
        mem_mb=12000,
    log:
        "logs/bazam/{sample}.log",
    wrapper:
        "v1.17.2/bio/bazam"

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

• bazam=1.0
• snakemake-wrapper-utils==0.5

Input/Output

Input:

• BAM/CRAM file
• reference genome

Output:

• fastq file

Authors

• Christopher Schröder

Code

__author__ = "Christopher Schröder"
__copyright__ = "Copyright 2022, Christopher Schröder"
__email__ = "christopher.schroeder@tu-dortmund.de"
__license__ = "MIT"

from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

java_opts = get_java_opts(snakemake)

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

# Extra parameters default value is an empty string
extra = snakemake.params.get("extra", "")

if bam.endswith(".cram"):
    if not (reference := snakemake.input.get("reference", "")):
        raise ValueError(
            "input 'reference' is required when working with CRAM input files"
        )
    reference_cmd = f"-Dsamjdk.reference_fasta={reference}"
else:
    reference_cmd = ""

# Extract arguments.
if reads := snakemake.output.get("reads", ""):
    out_cmd = f"-o {reads}"
elif (r1 := snakemake.output.get("r1", "")) and (r2 := snakemake.output.get("r2", "")):
    out_cmd = f"-r1 {r1} -r2 {r2}"
else:
    raise ValueError("either 'reads' or 'r1' and 'r2' must be specified in output")

shell("(bazam {java_opts} {reference_cmd} {extra} -bam {bam} {out_cmd}) {log}")