Hello,
I merged bam files using samtools merge -r out.bam in1.bam in2.bam ...
With -r option I got the RG tag for each read, as expected, good. However, the header of the merged bam does not have the @RG lines. So my question: Is there any off-the-shelf tools to add the @RG header lines once the reads have been tagged?
If not, the pipeline I have in mind goes along these lines:
- Scan the bam file and collect all the different RG tags
- Output the header of the bam file.
- Append the RG tags to the header the
- Reheader the original bam file.
Does it make sense?
Thanks
Dario
2 answers
I ended up writing a little script for this, if anyone is interested it is here:
Don't use samtools merge:
Note: Samtools' merge does not reconstruct the @RG dictionary in the header. Users
must provide the correct header with -h, or uses Picard which properly maintains
the header dictionary in merging.
•
written
by
Pierre Lindenbaum
and you can use http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups
•
written
by
Pierre Lindenbaum
Hi again Pierre. Sorry maybe I'm being thick. I'm not sure if/how to use AddOrReplaceReadGroup for this purpose as it complains that RG ID on SAMRecord not found in header. But that's what I want to do: Put the RG ID from the reads to the header.
java -jar ~/bin/picard.jar AddOrReplaceReadGroups I=rhh05082014_300ng.bam O=rhh05082014_300ng.new.bam LB=rhh05082014_300ng PL=illumina PU=mixed SM=rhh05082014 RGID=null
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 1, Read name NS500222:44:H15HDBGXX:1:11105:2110:3420, RG ID on SAMRecord not found in header: rhh088_A9_Pull1_300ng_Inp05082014.141215_NS500222_0044_H15HDBGXX.S1_L001.hg19.clean
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