Question: picard addorreplacereadgroups output issue
0
gravatar for Peter Chung
10 weeks ago by
Peter Chung70
Hong Kong
Peter Chung70 wrote:

I have a 189GB bam file and I need to add a readgroup in order to do downstream steps, so I used picard AddOrReplaceReadGroups to do it. Below is my command:

java -Xmx8g -jar $PICARD AddOrReplaceReadGroups \  
I=${name}.bam \
O=${name}.addRG.bam \
SORT_ORDER=coordinate \
RGID=${name} \
RGLB=lib1 \
RGPL=illumina \
RGPU=unit1 \
RGSM=${GP}.${name}

However, the output is only 14GB, I think there is sometimes wrong, but it didn't generate any error. Anyone can give me advice on that, thanks.

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by Peter Chung70
1

Hello Peter Chung ,

is there enough space left on your device? Do you have enough RAM? You could also try samtools addreplacerg:

$ samtools addreplacerg -r 'ID:${name}' -r 'LB:lib1' -r 'PL:illumina' -r 'PU:unit1' -r 'SM:${GP}.${name}' -o ${name}.addRG.bam ${name}.bam

fin swimmer

ADD REPLYlink written 10 weeks ago by finswimmer9.8k

Changed the label to "QUESTION" from "TOOL". The label TOOL is used to announce new tools to public.

ADD REPLYlink written 10 weeks ago by biokoala3.6k

I think there is sometimes wrong, but it didn't generate any error.

what were the last logs on the screen ?

ADD REPLYlink written 10 weeks ago by Pierre Lindenbaum116k

As you may already know, it's also possible (quicker and easier) to add read groups during the alignment step. That's something for your next analysis, then.

ADD REPLYlink written 10 weeks ago by WouterDeCoster36k
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