Where to find Microarray sample quality metrics in DRAGEN Array Cytogenetics and Emedgene

DRAGEN Array Cytogenetics Analysis

cyto call command generates gt_sample_summary file (CSV or JSON) which provides the following metrics:

Autosomal Call Rate

Call Rate

Log R Ratio Std Dev

Sex Estimate

cyto annotate command generates cyto annotation file (JSON) per sample to report sample-level, chromosome-level, and event-level metrics and annotations. See DRAGEN Array User Guide Cytogenetics Annotation JSON file for more details on the reported metrics.

Emedgene

Lab Tab

Under "SAMPLE QUALITY" section the following metrics are available:

Family Member

Quality

Sex Validation

Autosomal Call Rate

Call Rate

Log R Dev

For additional details regarding these metrics, see Emedgene User Guide: Lab tab and Sample quality section.

Under the Sample ID name, click Dragen report link to open Cytogenetics Array Report. This page contains sample and chromosomal information derived from the DRAGEN Array cyto annotation JSON file.

Sample Quality

Sample Sex

% LoH

Median CN

Call Rate

Log R Dev

Chromosome Quality

% Het

LRR Median

LRR Dev

% LoH

Median CN

Mean CN

Analysis Tools tab

Click on a variant from the list and the Variant page window pops up. Select Quality on the left menu. Under "Quality" section the following metrics are available:

VCF Filter

Likelihood Ratio

Mean LRR

Copy Number

Mosaic Fraction

CNV Quality

Size

Bin Count

For additional details regarding these metrics, see Emedgene User Guide Variant page and Quality tab.

For more information, see DRAGEN Array User Guide and Emedgene User Guide.

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