MOSDEPTH
fast BAM/CRAM depth calculation
Example
This wrapper can be used in the following way:
rule mosdepth:
input:
bam="aligned/{dataset}.bam",
bai="aligned/{dataset}.bam.bai",
output:
"mosdepth/{dataset}.mosdepth.global.dist.txt",
"mosdepth/{dataset}.per-base.bed.gz", # produced unless --no-per-base specified
summary="mosdepth/{dataset}.mosdepth.summary.txt", # this named output is required for prefix parsing
log:
"logs/mosdepth/{dataset}.log",
params:
extra="--fast-mode", # optional
# additional decompression threads through `--threads`
threads: 4 # This value - 1 will be sent to `--threads`
wrapper:
"v5.0.1/bio/mosdepth"
rule mosdepth_bed:
input:
bam="aligned/{dataset}.bam",
bai="aligned/{dataset}.bam.bai",
bed="test.bed",
output:
"mosdepth_bed/{dataset}.mosdepth.global.dist.txt",
"mosdepth_bed/{dataset}.mosdepth.region.dist.txt",
"mosdepth_bed/{dataset}.regions.bed.gz",
summary="mosdepth_bed/{dataset}.mosdepth.summary.txt", # this named output is required for prefix parsing
log:
"logs/mosdepth_bed/{dataset}.log",
params:
extra="--no-per-base --use-median", # optional
# additional decompression threads through `--threads`
threads: 4 # This value - 1 will be sent to `--threads`
wrapper:
"v5.0.1/bio/mosdepth"
rule mosdepth_by_threshold:
input:
bam="aligned/{dataset}.bam",
bai="aligned/{dataset}.bam.bai",
output:
"mosdepth_by_threshold/{dataset}.mosdepth.global.dist.txt",
"mosdepth_by_threshold/{dataset}.mosdepth.region.dist.txt",
"mosdepth_by_threshold/{dataset}.regions.bed.gz",
"mosdepth_by_threshold/{dataset}.thresholds.bed.gz", # needs to go with params.thresholds spec
summary="mosdepth_by_threshold/{dataset}.mosdepth.summary.txt", # this named output is required for prefix parsing
log:
"logs/mosdepth_by/{dataset}.log",
params:
by="500", # optional, window size, specifies --by for mosdepth.region.dist.txt and regions.bed.gz
thresholds="1,5,10,30", # optional, specifies --thresholds for thresholds.bed.gz
# additional decompression threads through `--threads`
threads: 4 # This value - 1 will be sent to `--threads`
wrapper:
"v5.0.1/bio/mosdepth"
rule mosdepth_quantize_precision:
input:
bam="aligned/{dataset}.bam",
bai="aligned/{dataset}.bam.bai",
output:
"mosdepth_quantize_precision/{dataset}.mosdepth.global.dist.txt",
"mosdepth_quantize_precision/{dataset}.quantized.bed.gz", # optional, needs to go with params.quantize spec
summary="mosdepth_quantize_precision/{dataset}.mosdepth.summary.txt", # this named output is required for prefix parsing
log:
"logs/mosdepth_quantize_precision/{dataset}.log",
params:
extra="--no-per-base", # optional
quantize="0:1:5:150", # optional, specifies --quantize for quantized.bed.gz
precision="5", # optional, set decimals of precision
# additional decompression threads through `--threads`
threads: 4 # This value - 1 will be sent to `--threads`
wrapper:
"v5.0.1/bio/mosdepth"
rule mosdepth_cram:
input:
bam="aligned/{dataset}.cram",
bai="aligned/{dataset}.cram.crai",
bed="test.bed",
fasta="genome.fasta",
output:
"mosdepth_cram/{dataset}.mosdepth.global.dist.txt",
"mosdepth_cram/{dataset}.mosdepth.region.dist.txt",
"mosdepth_cram/{dataset}.regions.bed.gz",
summary="mosdepth_cram/{dataset}.mosdepth.summary.txt", # this named output is required for prefix parsing
log:
"logs/mosdepth_cram/{dataset}.log",
params:
extra="--no-per-base --use-median", # optional
# additional decompression threads through `--threads`
threads: 4 # This value - 1 will be sent to `--threads`
wrapper:
"v5.0.1/bio/mosdepth"
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 by param allows to specify (integer) window-sizes (incompatible with input BED).
The threshold param allows to, for or each interval in –by, write number of bases covered by at least threshold bases. Specify multiple integer values separated by ‘,’.
The precision param allows to specify output floating point precision.
The extra param allows for additional program arguments.
For more information see, https://github.com/brentp/mosdepth
Software dependencies
mosdepth=0.3.8
Input/Output
Input:
BAM/CRAM files
reference genome (optional)
BED file (optional)
Output:
Several coverage summary files.
Code
__author__ = "William Rowell"
__copyright__ = "Copyright 2020, William Rowell"
__email__ = "wrowell@pacb.com"
__license__ = "MIT"
import sys
from snakemake.shell import shell
extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
bed = snakemake.input.get("bed", "")
by = snakemake.params.get("by", "")
if by:
if bed:
sys.exit(
"Either provide a bed input file OR a window size via params.by, not both."
)
else:
by = f"--by {by}"
if bed:
by = f"--by {bed}"
quantize_out = False
thresholds_out = False
regions_bed_out = False
region_dist_out = False
for file in snakemake.output:
if ".per-base." in file and "--no-per-base" in extra:
sys.exit(
"You asked not to generate per-base output (--no-per-base), but your rule specifies a '.per-base.' output file. Remove one of the two."
)
if ".quantized.bed.gz" in file:
quantize_out = True
if ".thresholds.bed.gz" in file:
thresholds_out = True
if ".mosdepth.region.dist.txt" in file:
region_dist_out = True
if ".regions.bed.gz" in file:
regions_bed_out = True
if by and not regions_bed_out:
sys.exit(
"You ask for by-region output. Please also specify *.regions.bed.gz as a rule output."
)
if by and not region_dist_out:
sys.exit(
"You ask for by-region output. Please also specify *.mosdepth.region.dist.txt as a rule output."
)
if (region_dist_out or regions_bed_out) and not by:
sys.exit(
"You specify *.regions.bed.gz and/or *.mosdepth.region.dist.txt as a rule output. You also need to ask for by-region output via 'input.bed' or 'params.by'."
)
quantize = snakemake.params.get("quantize", "")
if quantize:
if not quantize_out:
sys.exit(
"You ask for quantized output via params.quantize. Please also specify *.quantized.bed.gz as a rule output."
)
quantize = f"--quantize {quantize}"
if not quantize and quantize_out:
sys.exit(
"The rule has output *.quantized.bed.gz specified. Please also specify params.quantize to actually generate it."
)
thresholds = snakemake.params.get("thresholds", "")
if thresholds:
if not thresholds_out:
sys.exit(
"You ask for --thresholds output via params.thresholds. Please also specify *.thresholds.bed.gz as a rule output."
)
thresholds = f"--thresholds {thresholds}"
if not thresholds and thresholds_out:
sys.exit(
"The rule has output *.thresholds.bed.gz specified. Please also specify params.thresholds to actually generate it."
)
precision = snakemake.params.get("precision", "")
if precision:
precision = f"MOSDEPTH_PRECISION={precision}"
fasta = snakemake.input.get("fasta", "")
if fasta:
fasta = f"--fasta {fasta}"
# mosdepth takes additional threads through its option --threads
# One thread for mosdepth
# Other threads are *additional* decompression threads passed to the '--threads' argument
threads = "" if snakemake.threads <= 1 else "--threads {}".format(snakemake.threads - 1)
# named output summary = "*.mosdepth.summary.txt" is required
prefix = snakemake.output.summary.replace(".mosdepth.summary.txt", "")
shell(
"({precision} mosdepth {threads} {fasta} {by} {quantize} {thresholds} {extra} {prefix} {snakemake.input.bam}) {log}"
)