PFFailSummaryMetric

Metrics

Category Metrics

Overview

Metrics produced by the GetHiSeqXPFFailMetrics program. Used to diagnose lanes from HiSeqX Sequencing, providing the number and fraction of each of the reasons that reads could have not passed PF. Possible reasons are EMPTY (reads from empty wells with no template strand), POLYCLONAL (reads from wells that had more than one strand cloned in them), MISALIGNED (reads from wells that are near the edge of the tile), UNKNOWN (reads that didn't pass PF but couldn't be diagnosed)

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

Metric	Summary
TILE	The Tile that is described by this metric. Can be a string (like "All") to mean some marginal over tiles. *
READS	The total number of reads examined
PF_FAIL_READS	The number of non-PF reads in this tile.
PCT_PF_FAIL_READS	The fraction of PF_READS
PF_FAIL_EMPTY	The number of non-PF reads in this tile that are deemed empty.
PCT_PF_FAIL_EMPTY	The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
PF_FAIL_POLYCLONAL	The number of non-PF reads in this tile that are deemed multiclonal.
PCT_PF_FAIL_POLYCLONAL	The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
PF_FAIL_MISALIGNED	The number of non-PF reads in this tile that are deemed "misaligned".
PCT_PF_FAIL_MISALIGNED	The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
PF_FAIL_UNKNOWN	The number of non-PF reads in this tile that have not been classified.
PCT_PF_FAIL_UNKNOWN	The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).

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GATK version 4.6.2.0 built at Sun, 13 Apr 2025 13:21:43 -0400.