Add read group to header after samtools merge
2
1
Entering edit mode
7.0 years ago

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

samtools merge read group • 11k views
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4
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6.9 years ago

I ended up writing a little script for this, if anyone is interested is here addRGtoSAMHeader.py.

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6
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7.0 years ago

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.

 

but picard MergeSamFiles http://broadinstitute.github.io/picard/command-line-overview.html#MergeSamFiles

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0
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Thanks! I'll keep it mind and use picard in the future.

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1
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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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0
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Did you find a solution for this? I'm having the same issue.

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@Jordan My solution was to write the script linked in my answer below.
 

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