PICARD ADDORREPLACEREADGROUPS

Add or replace read groups with picard tools.

Software dependencies

  • picard ==2.9.2

Example

This wrapper can be used in the following way:

rule replace_rg:
    input:
        "mapped/{sample}.bam"
    output:
        "fixed-rg/{sample}.bam"
    log:
        "logs/picard/replace_rg/{sample}.log"
    params:
        "RGLB=lib1 RGPL=illumina RGPU={sample} RGSM={sample}"
    wrapper:
        "0.22.0/bio/picard/addorreplacereadgroups"

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

  • Johannes Köster

Code

__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "koester@jimmy.harvard.edu"
__license__ = "MIT"


from snakemake.shell import shell


shell("picard AddOrReplaceReadGroups {snakemake.params} I={snakemake.input} "
      "O={snakemake.output} &> {snakemake.log}")