Hello folks,
I struggled now a few days, but I don't get it:
What exactly is AddOrReplaceReadGroups doing?
http://picard.sourceforge.net/comman...laceReadGroups
Also, I actually can't find a good definition what a read group is. According to some descriptions on http://www.broadinstitute.org/gsa/wi...sked_Questions I infer that this the assignment of which reads belong to which lane and chip and so all reads in a read group have their own error model.
But what is now this tool doing? I'm using it in our pipeline, because without it one step breaks up. According to the description it replaces all groups. But why, what might be wrong with the old groups? How do they differ to the prior groups?
My call:
Thanks in advance,
Oliver
I struggled now a few days, but I don't get it:
What exactly is AddOrReplaceReadGroups doing?
http://picard.sourceforge.net/comman...laceReadGroups
Also, I actually can't find a good definition what a read group is. According to some descriptions on http://www.broadinstitute.org/gsa/wi...sked_Questions I infer that this the assignment of which reads belong to which lane and chip and so all reads in a read group have their own error model.
But what is now this tool doing? I'm using it in our pipeline, because without it one step breaks up. According to the description it replaces all groups. But why, what might be wrong with the old groups? How do they differ to the prior groups?
My call:
Code:
java -Djava.io.tmpdir='$TMPDIR' -jar /opt/biosw/picard-tools-1.45/AddOrReplaceReadGroups.jar RGLB=fastq/'$basename'.fastq RGPL=solexa RGPU=run RGSM=9111 I=output/'$basename'.bam O=output/'$basename'.sorted.bam SORT_ORDER=coordinate CREATE_INDEX=TRUE VALIDATION_STRINGENCY=LENIENT'
Oliver
Comment