Grep unique reads10/3/2023 ![]() The PU holds three types of information, the. Use for BQSR: ID is the lowest denominator that differentiates factors contributing to technical batch effects: therefore, a read group is effectively treated as a separate run of the instrument in data processing steps such as base quality score recalibration (unless you have PU defined), since they are assumed to share the same error model. In Illumina data, read group IDs are composed using the flowcell name and lane number, making them a globally unique identifier across all sequencing data in the world. Note that some Picard tools have the ability to modify IDs when merging SAM files in order to avoid collisions. It is referenced both in the read group definition line in the file header (starting with and in the RG:Z tag for each read record. This tag identifies which read group each read belongs to, so each read group's ID must be unique. Meaning of the read group fields required by GATK Samtools view -H sample.bam | grep prints the lines starting with within the header, e.g. To see the read group information for a BAM file, use the following command. See this article for common problems related to read groups. The GATK requires several read group fields to be present in input files and will fail with errors if this requirement is not satisfied. With this information in hand, we can mitigate the effects of those artifacts during the duplicate marking and base recalibration steps. These tags, when assigned appropriately, allow us to differentiate not only samples, but also various technical features that are associated with artifacts. ![]() Read groups are identified in the SAM/BAM /CRAM file by a number of tags that are defined in the official SAM specification. When multiplexing is involved, then each subset of reads originating from a separate library run on that lane will constitute a separate read group. In the simple case where a single library preparation derived from a single biological sample was run on a single lane of a flow cell, all the reads from that lane run belong to the same read group. There is no formal definition of what a 'read group' is, however in practice this term refers to a set of reads that are generated from a single run of a sequencing instrument.
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