BWA MEM
Map reads using bwa mem, with optional sorting using samtools or picard.
URL: http://bio-bwa.sourceforge.net/bwa.shtml
Example
This wrapper can be used in the following way:
rule bwa_mem:
input:
reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
output:
"mapped/{sample}.bam",
log:
"logs/bwa_mem/{sample}.log",
params:
extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
sorting="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:
"v3.7.0/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.
Notes
The extra param allows for additional arguments for bwa-mem.
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=0.7.17
samtools=1.19.2
picard-slim=3.1.1
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
FASTQ file(s)
reference genome
Output:
SAM/BAM/CRAM file
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"
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("sorting", "none")
sort_order = snakemake.params.get("sort_order", "coordinate")
sort_extra = snakemake.params.get("sort_extra", "")
samtools_opts = get_samtools_opts(snakemake, param_name="sort_extra")
java_opts = get_java_opts(snakemake)
index = snakemake.input.idx
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("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 {samtools_opts}"
elif sort == "samtools":
# Add name flag if needed.
if sort_order == "queryname":
sort_extra += " -n"
# Sort alignments using samtools sort.
pipe_cmd = "samtools sort {samtools_opts} {sort_extra} -T {tmpdir}"
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 mem"
" -t {snakemake.threads}"
" {extra}"
" {index}"
" {snakemake.input.reads}"
" | " + pipe_cmd + ") {log}"
)