Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Read groups

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    Genevieve Brandt

    Hello Rayz Ghimire, please see our document on Read Groups which should make things more clear. 

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    Rayz Ghimire

    Genevieve Brandt 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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    Rayz Ghimire

    Tiffany Miller any insights on my earlier question. 

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    Genevieve Brandt

    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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