Changing header of BAM

[thedamian]

Yes, I've already realised how to do this. Another option is to use Picard's AddOrReplaceReadGropus.jar.

java -jar AddOrReplaceReadGroups I=my.bam O=myGr.bam LB=whatever PL=illumina PU=whatever SM=whatever

Of course prior using AddOrReplaceReadGroups your .sam file needs to pass Picard's validation (ValidateSamFile.jar)

[colinmolter]

hi the damian,
when creating your sam file, you have to add read group header.
this should work:

bwa samse -r @RG\tID:IDa\tSM:SM\tPL:Illumina ref.fa my.sai my.fastq > my.sam
bests

colin

[thedamian]

Hi, I have the same problem as Hiroki.

I made a sam file using command:

bwa samse ref.fa my.sai my.fastq > my.sam

then, I have creaded .bam file:

samtools view -bS my.sam > my.bam

next, I have sorted my.bam file:

samtools sort my.bam my_sorted

Using GATK, I need to put a .bam file as an input.
According to the instructions from http://www.broadinstitute.org/gsa/wi...s_for_the_GATK I have used Picard's ReordereSam, to reorder reads:

java -jar ReordereSam.jar I=/path/my_sorted.bam O=/path/my_reordered.bam R=/path/ref.fa

Trying i.e.

java -jar GenomeAnalysisTK.jar -T DepthOfCoverage -R /paht/ref.fa -I /path/aln_reordered.bam

an error is returned:

##### ERROR MESSAGE: SAM/BAM file /path/my_reordered.bam is malformed: SAM file doesn't have any read groups defined in the header.  The GATK no longer supports SAM files without read groups

I have tried Picards AddOrReplaceReadGroups.jar and ReplaceSamHeader.jar but it didn't help me.

Any suggestions how to bulid proper .bam file for GATK?
thx

[desaila]

I've run into similar issues using GATK for bam files, and Picard. The option that always has helped me when I knew hte BAM file was "ok,"

java [args to jvm] GATK.jar [GAKT opts] VALIDATION_STRINGENCY=SILENT

[Hiroki]

Thanks ulz_peter!

I was told to use Picard from another guy.
Now I'm trying it.

Thank you so much anyways!

[ulz_peter]

you could easily change the header using samtools, but that won't solve the problem as the readgroup is necessary in each alignment section as well.
You could have a look in the AddOrReplaceReadGroup Utility of Picard:

http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGroups

I don't know if that changes the header as well but if not have a look here:

http://picard.sourceforge.net/command-line-overview.shtml#ReplaceSamHeader

[Hiroki]

Hello,

I apologize if my question is redundant....

I created bam files from fastq files by ELAND_standalone and tried to feed them to GATK. Then I got the following error message.
##### ERROR MESSAGE: SAM/BAM file reanalysis.bam is malformed: SAM file doesn't have any read groups defined in the header. The GATK no longer supports SAM files without read groups
##### ERROR -

How can I change the header? Samtools?

Thank you very much.

Hiroki