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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

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IlluminaPhasingMetrics Follow

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GATK Team
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Metrics

Category Metrics

Overview

Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis. Phasing refers to the fraction of molecules that fall behind or jump ahead (prephasing) during a read cycle. For each lane/template read # (i.e. FIRST, SECOND) combination we will store the median values of both the phasing and prephasing values for every tile in that lane/template read pair. @author jgentry

This table summarizes the values that are specific to this metric.

Metric Summary
LANE
 Illumina flowcell lane number
TYPE_NAME
 Defines an Illumina template read number (first or second)
PHASING_APPLIED
 Median phasing value across all tiles in a lane, applied to the first and second template reads
PREPHASING_APPLIED
 Median pre-phasing value across all tiles in a lane, applied to the first and second template reads

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GATK version 4.6.0.0-33-gdffedfb built at Wed, 23 Oct 2024 21:44:48 -0400.

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