Entering edit mode
5.7 years ago
elhlalisoufiane
▴
30
hi it's been a while since i have this problem : when i try to readgroup my sorted bam file using the following command
java -jar picard.jar AddOrReplaceReadGroups \
I=alnERR776198rmvDupSortindex.bam \
O=alnERR776198rmvDupSortindexRG.bam \
RGID=4 \
RGLB=lib1 \
RGPL=illumina \
RGPU=unit1 \
RGSM=ER776198
i get an empty output file pliiz someone help me with this .
Please use the formatting bar (especially the
code
option) to present your post better. I've done it for you this time. Also, try to avoid colloquialisms and IM slang spelling - it makes the post look extremely unprofessional.Try a non-numeric RGID and see if that fixes things.
thanks for the reply Devon Ryan i've tried BRCA for RGID but same output the file is empty
This is not an answer to your issue. Try this:
cpad0112 thnaks but when i apply your code i get this message [main] unrecognized command 'addreplacerg'
can you print the version of samtools ? version on my system:
then type
samtools addreplacerg
. This should throw all the options available for addreplacerg function. Make sure that you have recent/highest version of samtools available (via brew/conda/apt/dnf)i have the following header in my fastq file :
what would be the RGID RGLB RGPL RGPU RGSM ?
what was your original command ? what was the message displayed on screen ?
Pierre Lindenbaum i get the following message :
your alnERR776198rmvDupSortindex file is not a bam file. It's not a problem with picard but with the command that generated this bam file.
This message should have been part of your question. We cannot see your screen so you have to be as informative as possible when asking questions.
Which commands have you used to get to this bam?