Read groups
Hi, I am new to this and I'm trying to convert fastq to vcf. While using the bwa mem -R, the R represents read groups info, where can I actually find this information, and is there a way to proceed without it? I know the documentation says GATK will throw an error without this information.
Please any help will be appreciated.
Thank you
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Hello Rayz Ghimire, please see our document on Read Groups which should make things more clear.
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Genevieve Brandt (she/her) I did go through that documentation. It says samtools view -H input.bam | grep '@RG' should return the read group information. Is this true of all cases? If the read group meta data cannot be provided by the sequencing facility is there anyway we can get this data from the fastq itself?
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Tiffany Miller any insights on my earlier question.
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Rayz Ghimire Read groups are necessary for analysis with GATK. So, you will need to know some sequencing information about your samples.
Also important are the sample names and read group IDs. This is how GATK tracks samples during analysis.
Does this help answer your question?
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