BWA MEM¶
Map reads using bwa mem, with optional sorting using samtools or picard.
Software dependencies¶
- bwa ==0.7.17
- samtools ==1.9
- picard ==2.20.1
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:
"0.50.2/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.
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}"
)