Entering edit mode
4.2 years ago
User000
▴
690
Hello,
I would like to do variant calling with freebayes, however it requires the read groups. I am in a difficulty how to add the read groups to each of my 200 bam files, so that I can process it further.
workdir: "/path/to/workdir"
(SAMPLES,) =glob_wildcards('path/to/{sample}.bam')
rule all:
input:
expand("{sample}.mark.bam", sample=SAMPLES)
rule picard_markgroup:
input:
sortbam ="/path/to/{sample}.bam"
output:
dupbam = "{sample}.mark.bam"
shell:
"""
java -jar /Tools/picard/build/libs/picard.jar AddOrReplaceReadGroups I={input.sortbam} O={output.dupbam} SO=coordinate RGID=id RGLB=library RGPL=platform RGPU=machine RGSM=sample VALIDATION_STRINGENCY=SILENT
"""
This is giving me
@RG RGID=id RGLB=library RGPL=platform RGPU=machine RGSM=sample
Could you suggest how to modify this?