Question: picard addorreplacereadgroups output issue
0
gravatar for Peter Chung
7 months ago by
Peter Chung80
Hong Kong
Peter Chung80 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 7 months ago • written 7 months ago by Peter Chung80
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 7 months ago by finswimmer11k

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

ADD REPLYlink written 7 months ago by lakhujanivijay4.2k

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

what were the last logs on the screen ?

ADD REPLYlink written 7 months ago by Pierre Lindenbaum121k

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 7 months ago by WouterDeCoster40k
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: 933 users visited in the last hour