PICARD BEDTOINTERVALLIST

picard BedToIntervalList converts a BED file to Picard Interval List format.

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:
        "0.73.0/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 file
• dict: 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} "
)