Thread: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

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samtools-help

[Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Paul L. <p....@uq...> - 2011-04-11 05:00:11

I'm using Picards AddOrReplaceReadGroups to fix a sample issue but it
does not appear to be modify the library tag in the reads:

For example 
SKDP-31.3.ReCal.sort.old.bam  contains

HEADER
.
.
@RG	ID:SKDP-31.3	PU:illumina	LB:SKDP-31.3	SM:SKDP-31.3
.
.

and reads like :
ILLUMINA-A52086_0027_FC:7:49:13231:7611#0	355	chr1	69206	1	57M	=	69290
140	TCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCA
SSDDAEFDICIHCBDHFIEGGHIIDGIGDIEGGIGIIHEDIDCGGEHIGJHGCIISR	LB:Z:SKDP-31.3
MD:Z:57	PG:Z:novoalign	RG:Z:SKDP-31.3	AM:i:150	NM:i:0	SM:i:150	ZN:i:3
MQ:i:1	OQ:Z:IIIIIIIIIHIHIIIIIIIIIIIIIIIIIIHIIIIIIHHIGIIIIIIIIIIIIHIII
PQ:i:15	UQ:i:0	AS:i:0	ZS:Z:R	PU:Z:illumina




############### I want to swap SKDP-31.1 with SKDP-31.3 both sample and
library

I used 
java -jar picard-tools-1.42/AddOrReplaceReadGroups.jar
INPUT=SKDP-31.3.ReCal.sort.old.bam  OUTPUT=SKDP-31.1.ReCal.sort.bam
SORT_ORDER=coordinate RGID=SKDP-31.1 RGLB=SKDP-31.1 RGPL=illumina
RGPU=illumina RGSM=SKDP-31.1


I get 
.
.
@RG	ID:SKDP-31.1	PL:illumina	PU:illumina	LB:SKDP-31.1	SM:SKDP-31.1
.
.

ILLUMINA-A52086_0027_FC:7:10:5244:12288#0	147	chr1	69241	1	57M	=
69185	-112	CCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTC
SSGEFGCBJGEJFEGJBGHJHDCIJDJDICIDICFEHBDIEFDICIDECHEBGDDRS	LB:Z:SKDP-31.3
CC:Z:hr19	MD:Z:57	PG:Z:novoalign	RG:Z:SKDP-31.1	AM:i:150	NM:i:0	SM:i:150
ZN:i:3	CP:i:110829	MQ:i:1
OQ:Z:HHFIIIIBIIHIDHHIIIHIGIFIIHIFIHIHIHHIIFIIIIIIGIIIIHIIIIIIG	PQ:i:0
UQ:i:0	AS:i:0	ZS:Z:R	PU:Z:illumina


So the header and the RGID were changed as required BUT the RGLB was
changed in the header section but not in the reads LB:Z and should be
consistent with RG-LB tag in the header.

Any suggests on what I might be missing? I could find anything relevant
in the archives.  I'm using v1.42

Thanks
Paul

Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Mark A. D. <ma...@de...> - 2011-04-11 13:10:33

Hi all,

I see that the sam spec reserves LB as a tag in reads.  Isn't this redundant given the read group contains the sam value?  Why would one want to use such a tag, beyond minor convenience in avoiding looking up the read group for a read?  It seems to clutter up the spec -- perhaps it would be better to not include it at all?  

The simple solution to the problem below is to not use this LB tag on a read.

Best,

Mark

On Apr 11, 2011, at 12:45 AM, Paul Leo wrote:

> I'm using Picards AddOrReplaceReadGroups to fix a sample issue but it does not appear to be modify the library tag in the reads:
> 
> For example 
> SKDP-31.3.ReCal.sort.old.bam  contains
> 
> HEADER
> .
> .
> @RG	ID:SKDP-31.3	PU:illumina	LB:SKDP-31.3	SM:SKDP-31.3
> .
> .
> 
> and reads like :
> ILLUMINA-A52086_0027_FC:7:49:13231:7611#0	355	chr1	69206	1	57M	=	69290	140	TCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCA	SSDDAEFDICIHCBDHFIEGGHIIDGIGDIEGGIGIIHEDIDCGGEHIGJHGCIISR	LB:Z:SKDP-31.3	MD:Z:57	PG:Z:novoalign	RG:Z:SKDP-31.3	AM:i:150	NM:i:0	SM:i:150	ZN:i:3	MQ:i:1	OQ:Z:IIIIIIIIIHIHIIIIIIIIIIIIIIIIIIHIIIIIIHHIGIIIIIIIIIIIIHIII	PQ:i:15	UQ:i:0	AS:i:0	ZS:Z:R	PU:Z:illumina
> 
> 
> 
> 
> ############### I want to swap SKDP-31.1 with SKDP-31.3 both sample and library
> 
> I used 
> java -jar picard-tools-1.42/AddOrReplaceReadGroups.jar INPUT=SKDP-31.3.ReCal.sort.old.bam  OUTPUT=SKDP-31.1.ReCal.sort.bam  SORT_ORDER=coordinate RGID=SKDP-31.1 RGLB=SKDP-31.1 RGPL=illumina RGPU=illumina RGSM=SKDP-31.1
> 
> 
> I get 
> .
> .
> @RG	ID:SKDP-31.1	PL:illumina	PU:illumina	LB:SKDP-31.1	SM:SKDP-31.1
> .
> .
> 
> ILLUMINA-A52086_0027_FC:7:10:5244:12288#0	147	chr1	69241	1	57M	=	69185	-112	CCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTC	SSGEFGCBJGEJFEGJBGHJHDCIJDJDICIDICFEHBDIEFDICIDECHEBGDDRS	LB:Z:SKDP-31.3	CC:Z:hr19	MD:Z:57	PG:Z:novoalign	RG:Z:SKDP-31.1	AM:i:150	NM:i:0	SM:i:150	ZN:i:3	CP:i:110829	MQ:i:1	OQ:Z:HHFIIIIBIIHIDHHIIIHIGIFIIHIFIHIHIHHIIFIIIIIIGIIIIHIIIIIIG	PQ:i:0	UQ:i:0	AS:i:0	ZS:Z:R	PU:Z:illumina
> 
> 
> So the header and the RGID were changed as required BUT the RGLB was changed in the header section but not in the reads LB:Z and should be consistent with RG-LB tag in the header.
> 
> Any suggests on what I might be missing? I could find anything relevant in the archives.  I'm using v1.42
> 
> Thanks
> Paul
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev_______________________________________________
> Samtools-help mailing list
> Sam...@li...
> https://lists.sourceforge.net/lists/listinfo/samtools-help

Mark A. DePristo, Ph.D.
Manager, Medical and Population Genetics Analysis
Broad Institute of MIT and Harvard
dep...@br...
ma...@de...

Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Alec W. <al...@br...> - 2011-04-11 14:36:09

Hi Paul,

AddOrReplaceReadGroups does not touch the SAM record LB tag.  As Mark 
pointed out, this tag appears to be redundant with the read group LB 
value.  As far as I know, the SAM record LB tag is not used very much.

If you want to check out Picard source and modify AddOrReplaceReadGroups 
to do what you want, it is an easy change.

-Alec

On 4/11/11 12:45 AM, Paul Leo wrote:
> I'm using Picards AddOrReplaceReadGroups to fix a sample issue but it 
> does not appear to be modify the library tag in the reads:
>
> For example
> SKDP-31.3.ReCal.sort.old.bam  contains
>
> HEADER
> .
> .
> @RG ID:SKDP-31.3 PU:illumina LB:SKDP-31.3 SM:SKDP-31.3
> .
> .
>
> and reads like :
> ILLUMINA-A52086_0027_FC:7:49:13231:7611#0 355 chr1 69206 1 57M = 69290 
> 140 TCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCA 
> SSDDAEFDICIHCBDHFIEGGHIIDGIGDIEGGIGIIHEDIDCGGEHIGJHGCIISR 
> *LB:Z:SKDP-31.3* MD:Z:57 PG:Z:novoalign *RG:Z:SKDP-31.3* AM:i:150 
> NM:i:0 SM:i:150 ZN:i:3 MQ:i:1 
> OQ:Z:IIIIIIIIIHIHIIIIIIIIIIIIIIIIIIHIIIIIIHHIGIIIIIIIIIIIIHIII PQ:i:15 
> UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
>
>
>
>
> ############### I want to swap SKDP-31.1 with SKDP-31.3 both sample 
> and library
>
> I used
> java -jar picard-tools-1.42/AddOrReplaceReadGroups.jar 
> INPUT=SKDP-31.3.ReCal.sort.old.bam  OUTPUT=SKDP-31.1.ReCal.sort.bam  
> SORT_ORDER=coordinate RGID=SKDP-31.1 RGLB=SKDP-31.1 RGPL=illumina 
> RGPU=illumina RGSM=SKDP-31.1
>
>
> I get
> .
> .
> @RG ID:SKDP-31.1 PL:illumina PU:illumina LB:SKDP-31.1 SM:SKDP-31.1
> .
> .
>
> ILLUMINA-A52086_0027_FC:7:10:5244:12288#0 147 chr1 69241 1 57M = 69185 
> -112 CCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTC 
> SSGEFGCBJGEJFEGJBGHJHDCIJDJDICIDICFEHBDIEFDICIDECHEBGDDRS 
> *LB:Z:SKDP-31.3* CC:Z:hr19 MD:Z:57 PG:Z:novoalign *RG:Z:SKDP-31.1* 
> AM:i:150 NM:i:0 SM:i:150 ZN:i:3 CP:i:110829 MQ:i:1 
> OQ:Z:HHFIIIIBIIHIDHHIIIHIGIFIIHIFIHIHIHHIIFIIIIIIGIIIIHIIIIIIG PQ:i:0 
> UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
>
>
> So the header and the RGID were changed as required BUT the RGLB was 
> changed in the header section but not in the reads LB:Z and should be 
> consistent with RG-LB tag in the header.
>
> Any suggests on what I might be missing? I could find anything 
> relevant in the archives.  I'm using v1.42
>
> Thanks
> Paul
>
>
>
>
>
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
>
>
> _______________________________________________
> Samtools-help mailing list
> Sam...@li...
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>

Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Paul L. <p....@uq...> - 2011-04-13 00:48:49

Hi Alex and Mark
Thanks for the replies;

I agree the issue is unlikely to cause any problems (I can't say that I
use that tag myself). Nevertheless perhaps the authors will consider
making that minor modification in the next release, to be within the
letter of the SAM format specifications?

Thanks again.
Cheers
Paul




-----Original Message-----
From: Alec Wysoker <al...@br...>
To: Paul Leo <p....@uq...>
Cc: sam...@li...
<sam...@li...>
Subject: Re: [Samtools-help] Problem with PICARD :
AddOrReplaceReadGroups : library tag unchanged
Date: Tue, 12 Apr 2011 00:36:02 +1000

Hi Paul,

AddOrReplaceReadGroups does not touch the SAM record LB tag.  As Mark
pointed out, this tag appears to be redundant with the read group LB
value.  As far as I know, the SAM record LB tag is not used very much.

If you want to check out Picard source and modify AddOrReplaceReadGroups
to do what you want, it is an easy change.

-Alec

On 4/11/11 12:45 AM, Paul Leo wrote: 

> I'm using Picards AddOrReplaceReadGroups to fix a sample issue but it
> does not appear to be modify the library tag in the reads:
> 
> For example 
> SKDP-31.3.ReCal.sort.old.bam  contains
> 
> HEADER
> .
> .
> @RG ID:SKDP-31.3 PU:illumina LB:SKDP-31.3 SM:SKDP-31.3
> .
> .
> 
> and reads like :
> ILLUMINA-A52086_0027_FC:7:49:13231:7611#0 355 chr1 69206 1 57M = 69290
> 140 TCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCA
> SSDDAEFDICIHCBDHFIEGGHIIDGIGDIEGGIGIIHEDIDCGGEHIGJHGCIISR
> LB:Z:SKDP-31.3 MD:Z:57 PG:Z:novoalign RG:Z:SKDP-31.3 AM:i:150 NM:i:0
> SM:i:150 ZN:i:3 MQ:i:1
> OQ:Z:IIIIIIIIIHIHIIIIIIIIIIIIIIIIIIHIIIIIIHHIGIIIIIIIIIIIIHIII PQ:i:15
> UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
> 
> 
> 
> 
> ############### I want to swap SKDP-31.1 with SKDP-31.3 both sample
> and library
> 
> I used 
> java -jar picard-tools-1.42/AddOrReplaceReadGroups.jar
> INPUT=SKDP-31.3.ReCal.sort.old.bam  OUTPUT=SKDP-31.1.ReCal.sort.bam
> SORT_ORDER=coordinate RGID=SKDP-31.1 RGLB=SKDP-31.1 RGPL=illumina
> RGPU=illumina RGSM=SKDP-31.1
> 
> 
> I get 
> .
> .
> @RG ID:SKDP-31.1 PL:illumina PU:illumina LB:SKDP-31.1 SM:SKDP-31.1
> .
> .
> 
> ILLUMINA-A52086_0027_FC:7:10:5244:12288#0 147 chr1 69241 1 57M = 69185
> -112 CCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTC
> SSGEFGCBJGEJFEGJBGHJHDCIJDJDICIDICFEHBDIEFDICIDECHEBGDDRS
> LB:Z:SKDP-31.3 CC:Z:hr19 MD:Z:57 PG:Z:novoalign RG:Z:SKDP-31.1
> AM:i:150 NM:i:0 SM:i:150 ZN:i:3 CP:i:110829 MQ:i:1
> OQ:Z:HHFIIIIBIIHIDHHIIIHIGIFIIHIFIHIHIHHIIFIIIIIIGIIIIHIIIIIIG PQ:i:0
> UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
> 
> 
> So the header and the RGID were changed as required BUT the RGLB was
> changed in the header section but not in the reads LB:Z and should be
> consistent with RG-LB tag in the header.
> 
> Any suggests on what I might be missing? I could find anything
> relevant in the archives.  I'm using v1.42
> 
> Thanks
> Paul
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> 
> _______________________________________________
> Samtools-help mailing list
> Sam...@li...
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>

Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Mark A. D. <dep...@br...> - 2011-04-13 11:27:31

Hi Paul,

I think we're suggesting that the spec remove this problematical LB tag, rather than update the tool.  Heng / Richard -- is there some reason to officially endorse the use of this tag by putting it into the reserved list?

Best,

Mark

On Apr 12, 2011, at 8:47 PM, Paul Leo wrote:

> Hi Alex and Mark
> Thanks for the replies;
> 
> I agree the issue is unlikely to cause any problems (I can't say that I use that tag myself). Nevertheless perhaps the authors will consider  making that minor modification in the next release, to be within the letter of the SAM format specifications?
> 
> Thanks again.
> Cheers
> Paul
> 
> 
> 
> -----Original Message-----
> From: Alec Wysoker <al...@br...>
> To: Paul Leo <p....@uq...>
> Cc: sam...@li... <sam...@li...>
> Subject: Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged
> Date: Tue, 12 Apr 2011 00:36:02 +1000
> 
> Hi Paul,
> 
> AddOrReplaceReadGroups does not touch the SAM record LB tag.  As Mark pointed out, this tag appears to be redundant with the read group LB value.  As far as I know, the SAM record LB tag is not used very much.
> 
> If you want to check out Picard source and modify AddOrReplaceReadGroups to do what you want, it is an easy change.
> 
> -Alec
> 
> On 4/11/11 12:45 AM, Paul Leo wrote: 
>> I'm using Picards AddOrReplaceReadGroups to fix a sample issue but it does not appear to be modify the library tag in the reads:
>> 
>> For example 
>> SKDP-31.3.ReCal.sort.old.bam  contains
>> 
>> HEADER
>> .
>> .
>> @RG ID:SKDP-31.3 PU:illumina LB:SKDP-31.3 SM:SKDP-31.3
>> .
>> .
>> 
>> and reads like :
>> ILLUMINA-A52086_0027_FC:7:49:13231:7611#0 355 chr1 69206 1 57M = 69290 140 TCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCA SSDDAEFDICIHCBDHFIEGGHIIDGIGDIEGGIGIIHEDIDCGGEHIGJHGCIISR LB:Z:SKDP-31.3 MD:Z:57 PG:Z:novoalign RG:Z:SKDP-31.3 AM:i:150 NM:i:0 SM:i:150 ZN:i:3 MQ:i:1 OQ:Z:IIIIIIIIIHIHIIIIIIIIIIIIIIIIIIHIIIIIIHHIGIIIIIIIIIIIIHIII PQ:i:15 UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
>> 
>> 
>> 
>> 
>> ############### I want to swap SKDP-31.1 with SKDP-31.3 both sample and library
>> 
>> I used 
>> java -jar picard-tools-1.42/AddOrReplaceReadGroups.jar INPUT=SKDP-31.3.ReCal.sort.old.bam  OUTPUT=SKDP-31.1.ReCal.sort.bam  SORT_ORDER=coordinate RGID=SKDP-31.1 RGLB=SKDP-31.1 RGPL=illumina RGPU=illumina RGSM=SKDP-31.1
>> 
>> 
>> I get 
>> .
>> .
>> @RG ID:SKDP-31.1 PL:illumina PU:illumina LB:SKDP-31.1 SM:SKDP-31.1
>> .
>> .
>> 
>> ILLUMINA-A52086_0027_FC:7:10:5244:12288#0 147 chr1 69241 1 57M = 69185 -112 CCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTC SSGEFGCBJGEJFEGJBGHJHDCIJDJDICIDICFEHBDIEFDICIDECHEBGDDRS LB:Z:SKDP-31.3 CC:Z:hr19 MD:Z:57 PG:Z:novoalign RG:Z:SKDP-31.1 AM:i:150 NM:i:0 SM:i:150 ZN:i:3 CP:i:110829 MQ:i:1 OQ:Z:HHFIIIIBIIHIDHHIIIHIGIFIIHIFIHIHIHHIIFIIIIIIGIIIIHIIIIIIG PQ:i:0 UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
>> 
>> 
>> So the header and the RGID were changed as required BUT the RGLB was changed in the header section but not in the reads LB:Z and should be consistent with RG-LB tag in the header.
>> 
>> Any suggests on what I might be missing? I could find anything relevant in the archives.  I'm using v1.42
>> 
>> Thanks
>> Paul
>> 
>> 
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> Xperia(TM) PLAY
>> It's a major breakthrough. An authentic gaming
>> smartphone on the nation's most reliable network.
>> And it wants your games.
>> 
>> http://p.sf.net/sfu/verizon-sfdev
>> 
>> 
>> _______________________________________________
>> Samtools-help mailing list
>> 
>> Sam...@li...
>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>> 
>>   
>> 
> ------------------------------------------------------------------------------
> Forrester Wave Report - Recovery time is now measured in hours and minutes
> not days. Key insights are discussed in the 2010 Forrester Wave Report as
> part of an in-depth evaluation of disaster recovery service providers.
> Forrester found the best-in-class provider in terms of services and vision.
> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo_______________________________________________
> Samtools-help mailing list
> Sam...@li...
> https://lists.sourceforge.net/lists/listinfo/samtools-help

Mark A. DePristo, Ph.D.
Manager, Medical and Population Genetics Analysis
Broad Institute of MIT and Harvard
dep...@br...
ma...@de...

Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Heng Li <lh...@sa...> - 2011-04-13 13:44:24

I do not have a strong preference on this. I just worry LB might have been used by others.

Heng


On Apr 13, 2011, at 7:27 AM, Mark A. DePristo wrote:

> Hi Paul,
> 
> I think we're suggesting that the spec remove this problematical LB tag, rather than update the tool.  Heng / Richard -- is there some reason to officially endorse the use of this tag by putting it into the reserved list?
> 
> Best,
> 
> Mark
> 
> On Apr 12, 2011, at 8:47 PM, Paul Leo wrote:
> 
>> Hi Alex and Mark
>> Thanks for the replies;
>> 
>> I agree the issue is unlikely to cause any problems (I can't say that I use that tag myself). Nevertheless perhaps the authors will consider  making that minor modification in the next release, to be within the letter of the SAM format specifications?
>> 
>> Thanks again.
>> Cheers
>> Paul
>> 
>> 
>> 
>> -----Original Message-----
>> From: Alec Wysoker <al...@br...>
>> To: Paul Leo <p....@uq...>
>> Cc: sam...@li... <sam...@li...>
>> Subject: Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged
>> Date: Tue, 12 Apr 2011 00:36:02 +1000
>> 
>> Hi Paul,
>> 
>> AddOrReplaceReadGroups does not touch the SAM record LB tag.  As Mark pointed out, this tag appears to be redundant with the read group LB value.  As far as I know, the SAM record LB tag is not used very much.
>> 
>> If you want to check out Picard source and modify AddOrReplaceReadGroups to do what you want, it is an easy change.
>> 
>> -Alec
>> 
>> On 4/11/11 12:45 AM, Paul Leo wrote: 
>>> I'm using Picards AddOrReplaceReadGroups to fix a sample issue but it does not appear to be modify the library tag in the reads:
>>> 
>>> For example 
>>> SKDP-31.3.ReCal.sort.old.bam  contains
>>> 
>>> HEADER
>>> .
>>> .
>>> @RG ID:SKDP-31.3 PU:illumina LB:SKDP-31.3 SM:SKDP-31.3
>>> .
>>> .
>>> 
>>> and reads like :
>>> ILLUMINA-A52086_0027_FC:7:49:13231:7611#0 355 chr1 69206 1 57M = 69290 140 TCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCA SSDDAEFDICIHCBDHFIEGGHIIDGIGDIEGGIGIIHEDIDCGGEHIGJHGCIISR LB:Z:SKDP-31.3 MD:Z:57 PG:Z:novoalign RG:Z:SKDP-31.3 AM:i:150 NM:i:0 SM:i:150 ZN:i:3 MQ:i:1 OQ:Z:IIIIIIIIIHIHIIIIIIIIIIIIIIIIIIHIIIIIIHHIGIIIIIIIIIIIIHIII PQ:i:15 UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
>>> 
>>> 
>>> 
>>> 
>>> ############### I want to swap SKDP-31.1 with SKDP-31.3 both sample and library
>>> 
>>> I used 
>>> java -jar picard-tools-1.42/AddOrReplaceReadGroups.jar INPUT=SKDP-31.3.ReCal.sort.old.bam  OUTPUT=SKDP-31.1.ReCal.sort.bam  SORT_ORDER=coordinate RGID=SKDP-31.1 RGLB=SKDP-31.1 RGPL=illumina RGPU=illumina RGSM=SKDP-31.1
>>> 
>>> 
>>> I get 
>>> .
>>> .
>>> @RG ID:SKDP-31.1 PL:illumina PU:illumina LB:SKDP-31.1 SM:SKDP-31.1
>>> .
>>> .
>>> 
>>> ILLUMINA-A52086_0027_FC:7:10:5244:12288#0 147 chr1 69241 1 57M = 69185 -112 CCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTC SSGEFGCBJGEJFEGJBGHJHDCIJDJDICIDICFEHBDIEFDICIDECHEBGDDRS LB:Z:SKDP-31.3 CC:Z:hr19 MD:Z:57 PG:Z:novoalign RG:Z:SKDP-31.1 AM:i:150 NM:i:0 SM:i:150 ZN:i:3 CP:i:110829 MQ:i:1 OQ:Z:HHFIIIIBIIHIDHHIIIHIGIFIIHIFIHIHIHHIIFIIIIIIGIIIIHIIIIIIG PQ:i:0 UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
>>> 
>>> 
>>> So the header and the RGID were changed as required BUT the RGLB was changed in the header section but not in the reads LB:Z and should be consistent with RG-LB tag in the header.
>>> 
>>> Any suggests on what I might be missing? I could find anything relevant in the archives.  I'm using v1.42
>>> 
>>> Thanks
>>> Paul
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Xperia(TM) PLAY
>>> It's a major breakthrough. An authentic gaming
>>> smartphone on the nation's most reliable network.
>>> And it wants your games.
>>> 
>>> http://p.sf.net/sfu/verizon-sfdev
>>> 
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>>> 
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>>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>> 
>>> 
>>> 
>> ------------------------------------------------------------------------------
>> Forrester Wave Report - Recovery time is now measured in hours and minutes
>> not days. Key insights are discussed in the 2010 Forrester Wave Report as
>> part of an in-depth evaluation of disaster recovery service providers.
>> Forrester found the best-in-class provider in terms of services and vision.
>> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo_______________________________________________
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> 
> Mark A. DePristo, Ph.D.
> Manager, Medical and Population Genetics Analysis
> Broad Institute of MIT and Harvard
> dep...@br...
> ma...@de...
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Forrester Wave Report - Recovery time is now measured in hours and minutes
> not days. Key insights are discussed in the 2010 Forrester Wave Report as
> part of an in-depth evaluation of disaster recovery service providers.
> Forrester found the best-in-class provider in terms of services and vision.
> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
> _______________________________________________
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> Sam...@li...
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Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Paul L. <p....@uq...> - 2011-04-14 01:52:23

Hi Heng and Mark
Oh sorry I misunderstood.. a change in the Spec...I would be very
surprised if no one was using the LB tag in the reads ... I imagine it
would be useful in pulling library specific information from merged BAM
files (multiple runs with the same library etc). I would have thought
the change to the Picard update RGs would be a lot less painful.

The only real problem surey is compliance issues with data repositories;
if you remove LB  as a reserved read tag meaning "Library" someone is
bound to use LB for "something else" , would that cause problems?
Since shortread is not taking NGS data anymore you would seem ok there ;
I don't know if it is used anywhere in 1000genomes? I can't think of
anything else at the moment other than databases that use "ID" and "LB"
as a key and those users could maintain LB as a user defined tag ...

It would be nice  to modify the Picard add/change read groups utility so
you can update ANY tag in the reads/header including ones that users may
have generated themselves and mandatory ones, that would give legacy
users tools to maintain their existing tag usage (don't think it does
that right?) ,  and THEN drop the reserved word if you wish.


Cheers
Paul 




-----Original Message-----
From: Heng Li <lh...@sa...>
To: Mark A. DePristo <dep...@BR...>
Cc: Paul Leo <p....@uq...>, sam...@li...
<sam...@li...>
Subject: Re: [Samtools-help] Problem with PICARD :
AddOrReplaceReadGroups : library tag unchanged
Date: Wed, 13 Apr 2011 23:44:10 +1000


I do not have a strong preference on this. I just worry LB might have been used by others.

Heng


On Apr 13, 2011, at 7:27 AM, Mark A. DePristo wrote:

> Hi Paul,
> 
> I think we're suggesting that the spec remove this problematical LB tag, rather than update the tool.  Heng / Richard -- is there some reason to officially endorse the use of this tag by putting it into the reserved list?
> 
> Best,
> 
> Mark
> 
> On Apr 12, 2011, at 8:47 PM, Paul Leo wrote:
> 
>> Hi Alex and Mark
>> Thanks for the replies;
>> 
>> I agree the issue is unlikely to cause any problems (I can't say that I use that tag myself). Nevertheless perhaps the authors will consider  making that minor modification in the next release, to be within the letter of the SAM format specifications?
>> 
>> Thanks again.
>> Cheers
>> Paul
>> 
>> 
>> 
>> -----Original Message-----
>> From: Alec Wysoker <al...@br...>
>> To: Paul Leo <p....@uq...>
>> Cc: sam...@li... <sam...@li...>
>> Subject: Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged
>> Date: Tue, 12 Apr 2011 00:36:02 +1000
>> 
>> Hi Paul,
>> 
>> AddOrReplaceReadGroups does not touch the SAM record LB tag.  As Mark pointed out, this tag appears to be redundant with the read group LB value.  As far as I know, the SAM record LB tag is not used very much.
>> 
>> If you want to check out Picard source and modify AddOrReplaceReadGroups to do what you want, it is an easy change.
>> 
>> -Alec
>> 
>> On 4/11/11 12:45 AM, Paul Leo wrote: 
>>> I'm using Picards AddOrReplaceReadGroups to fix a sample issue but it does not appear to be modify the library tag in the reads:
>>> 
>>> For example 
>>> SKDP-31.3.ReCal.sort.old.bam  contains
>>> 
>>> HEADER
>>> .
>>> .
>>> @RG ID:SKDP-31.3 PU:illumina LB:SKDP-31.3 SM:SKDP-31.3
>>> .
>>> .
>>> 
>>> and reads like :
>>> ILLUMINA-A52086_0027_FC:7:49:13231:7611#0 355 chr1 69206 1 57M = 69290 140 TCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCA SSDDAEFDICIHCBDHFIEGGHIIDGIGDIEGGIGIIHEDIDCGGEHIGJHGCIISR LB:Z:SKDP-31.3 MD:Z:57 PG:Z:novoalign RG:Z:SKDP-31.3 AM:i:150 NM:i:0 SM:i:150 ZN:i:3 MQ:i:1 OQ:Z:IIIIIIIIIHIHIIIIIIIIIIIIIIIIIIHIIIIIIHHIGIIIIIIIIIIIIHIII PQ:i:15 UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
>>> 
>>> 
>>> 
>>> 
>>> ############### I want to swap SKDP-31.1 with SKDP-31.3 both sample and library
>>> 
>>> I used 
>>> java -jar picard-tools-1.42/AddOrReplaceReadGroups.jar INPUT=SKDP-31.3.ReCal.sort.old.bam  OUTPUT=SKDP-31.1.ReCal.sort.bam  SORT_ORDER=coordinate RGID=SKDP-31.1 RGLB=SKDP-31.1 RGPL=illumina RGPU=illumina RGSM=SKDP-31.1
>>> 
>>> 
>>> I get 
>>> .
>>> .
>>> @RG ID:SKDP-31.1 PL:illumina PU:illumina LB:SKDP-31.1 SM:SKDP-31.1
>>> .
>>> .
>>> 
>>> ILLUMINA-A52086_0027_FC:7:10:5244:12288#0 147 chr1 69241 1 57M = 69185 -112 CCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTC SSGEFGCBJGEJFEGJBGHJHDCIJDJDICIDICFEHBDIEFDICIDECHEBGDDRS LB:Z:SKDP-31.3 CC:Z:hr19 MD:Z:57 PG:Z:novoalign RG:Z:SKDP-31.1 AM:i:150 NM:i:0 SM:i:150 ZN:i:3 CP:i:110829 MQ:i:1 OQ:Z:HHFIIIIBIIHIDHHIIIHIGIFIIHIFIHIHIHHIIFIIIIIIGIIIIHIIIIIIG PQ:i:0 UQ:i:0 AS:i:0 ZS:Z:R PU:Z:illumina
>>> 
>>> 
>>> So the header and the RGID were changed as required BUT the RGLB was changed in the header section but not in the reads LB:Z and should be consistent with RG-LB tag in the header.
>>> 
>>> Any suggests on what I might be missing? I could find anything relevant in the archives.  I'm using v1.42
>>> 
>>> Thanks
>>> Paul
>>> 
>>> 
>>> 
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Xperia(TM) PLAY
>>> It's a major breakthrough. An authentic gaming
>>> smartphone on the nation's most reliable network.
>>> And it wants your games.
>>> 
>>> http://p.sf.net/sfu/verizon-sfdev
>>> 
>>> 
>>> _______________________________________________
>>> Samtools-help mailing list
>>> 
>>> Sam...@li...
>>> https://lists.sourceforge.net/lists/listinfo/samtools-help
>>> 
>>> 
>>> 
>> ------------------------------------------------------------------------------
>> Forrester Wave Report - Recovery time is now measured in hours and minutes
>> not days. Key insights are discussed in the 2010 Forrester Wave Report as
>> part of an in-depth evaluation of disaster recovery service providers.
>> Forrester found the best-in-class provider in terms of services and vision.
>> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo_______________________________________________
>> Samtools-help mailing list
>> Sam...@li...
>> https://lists.sourceforge.net/lists/listinfo/samtools-help
> 
> Mark A. DePristo, Ph.D.
> Manager, Medical and Population Genetics Analysis
> Broad Institute of MIT and Harvard
> dep...@br...
> ma...@de...
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> ------------------------------------------------------------------------------
> Forrester Wave Report - Recovery time is now measured in hours and minutes
> not days. Key insights are discussed in the 2010 Forrester Wave Report as
> part of an in-depth evaluation of disaster recovery service providers.
> Forrester found the best-in-class provider in terms of services and vision.
> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
> _______________________________________________
> Samtools-help mailing list
> Sam...@li...
> https://lists.sourceforge.net/lists/listinfo/samtools-help

Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Peter <pe...@ma...> - 2011-04-14 08:48:55

On Thu, Apr 14, 2011 at 2:23 AM, Paul Leo <p....@uq...> wrote:
>
> Hi Heng and Mark
> Oh sorry I misunderstood.. a change in the Spec...I would be very surprised
> if no one was using the LB tag in the reads ... I imagine it would be useful in
> pulling library specific information from merged BAM files (multiple runs with
> the same library etc). I would have thought the change to the Picard update
> RGs would be a lot less painful.
>
> The only real problem surey is compliance issues with data repositories; if
> you remove LB  as a reserved read tag meaning "Library" someone is
> bound to use LB for "something else" , would that cause problems?
> Since shortread is not taking NGS data anymore you would seem ok there ;

However it might for the DDBJ and EBI, whose ENA short read archive is
still on going. And they are looking at BAM as a file format, or so I
understand.

Peter

Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Mark A. D. <ma...@de...> - 2011-04-14 10:46:01

Hi all,

The reason I believe the read-level tag is a bad idea is that the LB information is already specified in the RG header entry, and each read really should have a read group identify.  The right way to get LB information is to put it into the RG, put on a RG tag in each read, and read.tag -> RG -> RG.LB whenever you need it.  Including an space-expense, redundant option in the official spec is confusing and generates additional work for tool developers.  

I really hope that the repositories haven't used LB (at large space cost) to encode redundant information to the RG information.  This concern is all the more reason to remove it from the spec. 

Best,

Mark

On Apr 14, 2011, at 4:48 AM, Peter wrote:

> On Thu, Apr 14, 2011 at 2:23 AM, Paul Leo <p....@uq...> wrote:
>> 
>> Hi Heng and Mark
>> Oh sorry I misunderstood.. a change in the Spec...I would be very surprised
>> if no one was using the LB tag in the reads ... I imagine it would be useful in
>> pulling library specific information from merged BAM files (multiple runs with
>> the same library etc). I would have thought the change to the Picard update
>> RGs would be a lot less painful.
>> 
>> The only real problem surey is compliance issues with data repositories; if
>> you remove LB  as a reserved read tag meaning "Library" someone is
>> bound to use LB for "something else" , would that cause problems?
>> Since shortread is not taking NGS data anymore you would seem ok there ;
> 
> However it might for the DDBJ and EBI, whose ENA short read archive is
> still on going. And they are looking at BAM as a file format, or so I
> understand.
> 
> Peter

Mark A. DePristo, Ph.D.
Manager, Medical and Population Genetics Analysis
Broad Institute of MIT and Harvard
dep...@br...
ma...@de...

Re: [Samtools-help] Problem with PICARD : AddOrReplaceReadGroups : library tag unchanged

From: Goncalo A. <go...@um...> - 2011-04-14 12:47:31

I agree with Mark on this one. Having multiple redundant ways of encoding
the same information also makes it more complex to consume a BAM and to
verify it includes key bits of information.

Gonçalo


> -----Original Message-----
> From: Mark A. DePristo [mailto:ma...@de...]
> Sent: Thursday, April 14, 2011 6:46 AM
> To: pe...@ma...
> Cc: sam...@li...
> Subject: Re: [Samtools-help] Problem with PICARD :
> AddOrReplaceReadGroups : library tag unchanged
> 
> Hi all,
> 
> The reason I believe the read-level tag is a bad idea is that the LB
information
> is already specified in the RG header entry, and each read really should
have
> a read group identify.  The right way to get LB information is to put it
into the
> RG, put on a RG tag in each read, and read.tag -> RG -> RG.LB whenever you
> need it.  Including an space-expense, redundant option in the official
spec is
> confusing and generates additional work for tool developers.
> 
> I really hope that the repositories haven't used LB (at large space cost)
to
> encode redundant information to the RG information.  This concern is all
the
> more reason to remove it from the spec.
> 
> Best,
> 
> Mark
> 
> On Apr 14, 2011, at 4:48 AM, Peter wrote:
> 
> > On Thu, Apr 14, 2011 at 2:23 AM, Paul Leo <p....@uq...> wrote:
> >>
> >> Hi Heng and Mark
> >> Oh sorry I misunderstood.. a change in the Spec...I would be very
> >> surprised if no one was using the LB tag in the reads ... I imagine
> >> it would be useful in pulling library specific information from
> >> merged BAM files (multiple runs with the same library etc). I would
> >> have thought the change to the Picard update RGs would be a lot less
> painful.
> >>
> >> The only real problem surey is compliance issues with data
> >> repositories; if you remove LB  as a reserved read tag meaning
> >> "Library" someone is bound to use LB for "something else" , would that
> cause problems?
> >> Since shortread is not taking NGS data anymore you would seem ok
> >> there ;
> >
> > However it might for the DDBJ and EBI, whose ENA short read archive is
> > still on going. And they are looking at BAM as a file format, or so I
> > understand.
> >
> > Peter
> 
> Mark A. DePristo, Ph.D.
> Manager, Medical and Population Genetics Analysis Broad Institute of MIT
> and Harvard dep...@br... ma...@de...
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
>
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