Question: How treat a Bam file with mutiple read groups (RG)

Hi everyone, I am pretty new to the NGS data analysis. I have downloaded a WES dataset at BAM file format from SRA database. I try to mark duplicates in bam file using MarkDuplicates command at Picard . However, I encountered an error in terminal "error parsing sam header. @rg line missing sm tag". I tough that there is an error in @RG tag. So I run a command in terminal i.e. "samtools view -H SRR1693634_NC_000005.9.sorted.bam | grep '@RG' to see rg tag". Output is below

@RG ID:FGC0630.4.ACTGAT
@RG ID:FGC0639.8.ACTGAT
@RG ID:FGC0639.7.ACTGAT
@RG ID:FGC0639.4.ACTGAT
@RG ID:FGC0639.6.ACTGAT
@RG ID:FGC0639.5.ACTGAT

Now I have two questions:

1. What is meaning of the several read groups for a single sample? Are MarkDuplicates results for a sample with single RG are similar to the that sample with multiple RGs?

2. RGs in my sample lacks some necessary information such as RGID, RGLB, RGPL, RGPU, RGSM. How can I obtain and then add these information to the bam file for each RG? As you know AddOrReplaceReadGroups in Picard only treats sample with a single RG.

Answers

  • AdelaideRAdelaideR Unconfirmed, Member, Broadie, Moderator admin

    Hello @mohamadzamani

    You might see this if the original genome file designated each chromosome with a separate read group.

    It is possible to fix this by adding a generic read group using:

    gatk AddOrReplaceReadGroups
    

    This will replace all the missing information.

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