GATK COLLECTREADCOUNTS
Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval.
URL: https://gatk.broadinstitute.org/hc/en-us/articles/360037592671-CollectReadCounts
Example
This wrapper can be used in the following way:
rule collectreadcounts:
input:
bam=["mapped/a.bam"],
intervals=["a.interval_list"],
output:
counts="a.counts.hdf5",
log:
"logs/gatk/collectreadcounts.log",
params:
extra="", # optional
java_opts="", # optional
resources:
mem_mb=1024,
wrapper:
"v3.9.0/bio/gatk/collectreadcounts"
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
gatk4=4.5.0.0
snakemake-wrapper-utils=0.6.2
Input/Output
Input:
bam
: BAM/SAM/CRAM file containing readsintervals
: one or more genomic intervals over which to operate
Output:
counts
: output file for read counts, tsv or hdf5
Params
mergingRule
: interval merging rule for abutting intervals (default, OVERLAPPING_ONLY)java_opts
: additional arguments to be passed to the java compiler, e.g. “-XX:ParallelGCThreads=10” (not for -XmX or -Djava.io.tmpdir, since they are handled automatically).extra
: additional program arguments.
Code
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2023, Patrik Smed"
__email__ = "patrik.smeds@gmail.com"
__license__ = "MIT"
import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)
mergingRule = snakemake.params.get("mergingRule", "OVERLAPPING_ONLY")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)
with tempfile.TemporaryDirectory() as tmpdir:
shell(
"gatk --java-options '{java_opts}' CollectReadCounts"
" -I {snakemake.input.bam}"
" -L {snakemake.input.intervals}"
" --interval-merging-rule {mergingRule}"
" {extra}"
" --tmp-dir {tmpdir}"
" --output {snakemake.output.counts}"
" {log}"
)