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DNA Library QC Metrics for Small Variant Calling

Metric

Description

Recommended Threshold

PCT_CHIMERIC_READS (%)

Percentage of unique reads that are part of a chimeric alignment (for example, half of the read maps to one location and the other half maps to a nonsequential location) out of the total number of mapped unique reads.

≤ 3.5

MEDIAN_INSERT_SIZE (bp)

Median of fragment sizes calculated from read alignments.

≥ 70

PCT_EXON_250X (%)

Percentage of exonic bases in gVCF that have greater than or equal to 250X coverage.

≥ 81.3
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