what is a read group?

wenhuang · 09-28-2011, 07:18 AM

Hi,

I am sure this is a silly question, but what is a read group in bam files? A lane? a flow cell? a library? or any meaningful thing that can group reads together?

Thanks!

Wen

danielsbrewer · 09-28-2011, 08:46 AM

http://seqanswers.com/forums/showthread.php?t=4994

rskr · 09-28-2011, 03:25 PM

I define the term read-group as a set of reads that are the result of the exact same wet lab protocol, from isolation of samples to attached barcodes and indexing. Informally I use the term read-group when referring to a GaIIx lane or HiSeq index.

Do they use that same convention?

weeseda · 04-02-2014, 10:39 AM

I've checked out the samtools man and other documents, but I'm still confussed on the read group line.

I am looking at 3 populations each of 8 individuals and want to do some SNP calling and downstream analysis. All 24 individuls were barcoded and run in one illumina lane.

To keep track of individuals and populations how would I set up the readgroup line? RG= population name and SM= individual (as below)? or is it even possible to keep track of both?

Thanks in advance for any insight!

rg.txt file for use with following command: samtools merge -rh rg.txt merged.bam *.bam

@RG ID:Pop1 SM:27861 PL:Illumina
@RG ID:Pop1 SM:27862 PL:Illumina
@RG ID:Pop2 SM:27863 PL:Illumina
@RG ID:Pop2 SM:27864 PL:Illumina
@RG ID:Pop3 SM:27865 PL:Illumina
@RG ID:Pop3 SM:27866 PL:Illumina
.
.
.

kmcarr · 04-03-2014, 06:46 AM

Quote:

Originally Posted by weeseda

I've checked out the samtools man and other documents, but I'm still confussed on the read group line.

I am looking at 3 populations each of 8 individuals and want to do some SNP calling and downstream analysis. All 24 individuls were barcoded and run in one illumina lane.

To keep track of individuals and populations how would I set up the readgroup line? RG= population name and SM= individual (as below)? or is it even possible to keep track of both?

Thanks in advance for any insight!

rg.txt file for use with following command: samtools merge -rh rg.txt merged.bam *.bam

Code:

@RG	ID:Pop1	SM:27861	PL:Illumina
@RG	ID:Pop1	SM:27862	PL:Illumina
@RG	ID:Pop2	SM:27863	PL:Illumina
@RG	ID:Pop2	SM:27864	PL:Illumina
@RG	ID:Pop3	SM:27865	PL:Illumina
@RG	ID:Pop3	SM:27866	PL:Illumina

.
.
.

Each read group you define must have a unique ID. Your example does not, it uses each ID (Pop1, Pop2, Pop3) twice. Try something like this:

Code:

@RG	ID:1	SM:Pop1-27861	PL:Illumina
@RG	ID:2	SM:Pop1-27862	PL:Illumina
@RG	ID:3	SM:Pop2-27863	PL:Illumina
@RG	ID:4	SM:Pop2-27864	PL:Illumina
@RG	ID:5	SM:Pop3-27865	PL:Illumina
@RG	ID:6	SM:Pop3-27866	PL:Illumina

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09-28-2011, 07:18 AM	#1
wenhuang Member Location: Raleigh, NC Join Date: Feb 2010 Posts: 30	what is a read group? Hi, I am sure this is a silly question, but what is a read group in bam files? A lane? a flow cell? a library? or any meaningful thing that can group reads together? Thanks! Wen

09-28-2011, 08:46 AM	#2
danielsbrewer Member Location: UK Join Date: Feb 2009 Posts: 33	http://seqanswers.com/forums/showthread.php?t=4994

09-28-2011, 03:25 PM	#3
rskr Senior Member Location: Santa Fe, NM Join Date: Oct 2010 Posts: 250	I define the term read-group as a set of reads that are the result of the exact same wet lab protocol, from isolation of samples to attached barcodes and indexing. Informally I use the term read-group when referring to a GaIIx lane or HiSeq index. Do they use that same convention?

04-02-2014, 10:39 AM	#4
weeseda Junior Member Location: Alabama, US Join Date: Dec 2011 Posts: 5	I've checked out the samtools man and other documents, but I'm still confussed on the read group line. I am looking at 3 populations each of 8 individuals and want to do some SNP calling and downstream analysis. All 24 individuls were barcoded and run in one illumina lane. To keep track of individuals and populations how would I set up the readgroup line? RG= population name and SM= individual (as below)? or is it even possible to keep track of both? Thanks in advance for any insight! rg.txt file for use with following command: samtools merge -rh rg.txt merged.bam *.bam @RG ID:Pop1 SM:27861 PL:Illumina @RG ID:Pop1 SM:27862 PL:Illumina @RG ID:Pop2 SM:27863 PL:Illumina @RG ID:Pop2 SM:27864 PL:Illumina @RG ID:Pop3 SM:27865 PL:Illumina @RG ID:Pop3 SM:27866 PL:Illumina . . .