PICARD COLLECTTARGETEDPCRMETRICS¶
Collect metric information for target pcr metrics runs, with picard tools.
Software dependencies¶
- picard ==2.22.1
Example¶
This wrapper can be used in the following way:
rule CollectTargetedPcrMetrics:
input:
bam="mapped/{sample}.bam",
amplicon_intervals="amplicon.list",
target_intervals="target.list"
output:
"stats/{sample}.pcr.txt"
log:
"logs/picard/collecttargetedpcrmetrics/{sample}.log"
params:
extra=""
wrapper:
"0.59.1/bio/picard/collecttargetedpcrmetrics"
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¶
- Patrik Smeds
Code¶
__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2019, Patrik Smeds"
__email__ = "patrik.smeds@mail.com"
__license__ = "MIT"
from snakemake.shell import shell
log = snakemake.log_fmt_shell()
extra = snakemake.params.get("extra", "")
shell(
"picard CollectTargetedPcrMetrics "
"{extra} "
"INPUT={snakemake.input.bam} "
"OUTPUT={snakemake.output[0]} "
"AMPLICON_INTERVALS={snakemake.input.amplicon_intervals} "
"TARGET_INTERVALS={snakemake.input.target_intervals} "
"{log}"
)