Question: Picard AddOrReplaceReadGroups unable to read my argument?
0
gravatar for quachtina96
3.7 years ago by
quachtina9630
United States
quachtina9630 wrote:

Hi, I am trying to run Picard's AddOrReplaceReadGroups on a bam file called exome_mtExtractremap.csort.bam (code below). the error messages states "ERROR: Option 'RGPL' is required.", however I have included RGPL, so I don't understand why it is occuring.

I've tried RGLB=ILLUMINA, RGLB="ILLUMINA", and RGLB=illumina. What am I doing wrong?

 

 

i=exome_mtExtractremap.csort.bam
java -Xmx2g \
-Djava.io.tmpdir=`pwd`/tmp \
-jar /opt/applications/picard/current/AddOrReplaceReadGroups.jar \
INPUT="${i}" \
OUTPUT="${i}.rg.bam" \
SORT_ORDER=coordinate \
RGLB="$(echo $OUTPUT | sed 's/_mtExtractremap.csort.bam.rg.bam//')" \
RGPL="illumina" \
RGPU="L002" \
RGSM="${RGLB}" \
RGID="${RGLB}_${RGPU}";

 

 

read group picard • 2.1k views
ADD COMMENTlink written 3.7 years ago by quachtina9630

I suspect there something wrong in the line just *before" RGPL

ADD REPLYlink written 3.7 years ago by Pierre Lindenbaum118k
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