Question: Picard AddOrReplaceReadGroups unable to read my argument?
0
gravatar for quachtina96
4.2 years ago by
quachtina9640
United States
quachtina9640 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 • 2.4k views
ADD COMMENTlink written 4.2 years ago by quachtina9640

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

ADD REPLYlink written 4.2 years ago by Pierre Lindenbaum122k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1212 users visited in the last hour