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Obtaining read group information from the fastq files

saikat10MAy1995saikat10MAy1995 IndiaMember
edited March 2017 in Ask the GATK team

I have fastq files with headers
@SN963:294:C847FACXX:1:1106:1077:2087 1:N:0:AGGCAGAA (File name -DYP26_blood_S3_L001_R1_001.fastq)
and
@SN963:294:C847FACXX:1:1106:1077:2087 2:N:0:AGGCAGAA (File name- DYP26_blood_S3_L001_R2_001.fastq)
these are pairs of the same sample.
But, I need read group information for analyzing using GATK, which I don't have. how do I get the read group to include in the BWA step.

Answers

  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @saikat10MAy1995,

    You can assign read group ID fields arbitrarily, e.g. A, B, C.... If you're interested in how we assign them, I've broken down the components here, in the section titled "Deriving ID and PU fields from read names".

    I would avoid including the @ sign or other non-alphanumeric symbols in read group ID names.

  • FdoSRFdoSR Member

    Dear All,

    I am following the steps indicated in the document entitled "From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline", but I have a doubt regarding a particular part:

    I have fastq files from Paired-End of a WGS made with illumina recently. However, it is not clear to me how the read group (@RG) is created. Is it a file that contains a line that starts with @RG and that includes the information of each fastq file? Is one line of those for each file Fw and Rv?

    Thanks in advance.

    Best regards

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @FdoSR

    Read groups are created in the SAM/BAM /CRAM files and they can be identified by 'RG' tag. These tags are created based on information such as flowcell + lane name and number, sequencing platform, sample name, library prep ID. These tags, when assigned appropriately, allow us to differentiate not only samples, but also various technical features that are associated with artifacts. With this information in hand, we can mitigate the effects of those artifacts during the duplicate marking and base recalibration steps.

    You can create the tags by using AddOrReplaceReadGroups function of picard tools. For more information on that: http://broadinstitute.github.io/picard/command-line-overview.html#AddOrReplaceReadGroups

    For information on use of read groups please follow this link: https://software.broadinstitute.org/gatk/documentation/article?id=6472

    I hope this helps.

    Regards
    Bhanu

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