PICARD BEDTOINTERVALLIST¶
picard BedToIntervalList converts a BED file to Picard Interval List format.
URL:
Example¶
This wrapper can be used in the following way:
rule bed_to_interval_list:
input:
bed="resources/a.bed",
dict="resources/genome.dict"
output:
"a.interval_list"
log:
"logs/picard/bedtointervallist/a.log"
params:
# optional parameters
"SORT=true " # sort output interval list before writing
# optional specification of memory usage of the JVM that snakemake will respect with global
# resource restrictions (https://snakemake.readthedocs.io/en/latest/snakefiles/rules.html#resources)
# and which can be used to request RAM during cluster job submission as `{resources.mem_mb}`:
# https://snakemake.readthedocs.io/en/latest/executing/cluster.html#job-properties
resources:
mem_mb=1024
wrapper:
"0.80.1/bio/picard/bedtointervallist"
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¶
picard==2.22.1
snakemake-wrapper-utils==0.1.3
Input/Output¶
Input:
bed
: region filedict
: genome dictionary file (from samtools dict or picard CreateSequenceDictionary )
Output:
- interval_list Picard format
Authors¶
- Fabian Kilpert
Code¶
__author__ = "Fabian Kilpert"
__copyright__ = "Copyright 2020, Fabian Kilpert"
__email__ = "fkilpert@gmail.com"
__license__ = "MIT"
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts
log = snakemake.log_fmt_shell()
extra = snakemake.params
java_opts = get_java_opts(snakemake)
shell(
"picard BedToIntervalList "
"{java_opts} {extra} "
"INPUT={snakemake.input.bed} "
"SEQUENCE_DICTIONARY={snakemake.input.dict} "
"OUTPUT={snakemake.output} "
"{log} "
)