VCF Quality Control

Overview

To evaluate the quality of a vcf file, different metrics are calculated using granite SVqcVCF.

The metrics currently available are:

• Variant types distribution per sample
• Total variant counts per sample

Definitions

Variant Types Distribution

Total number of variants classified by type as:

• DELetion (SVTYPE=DEL)
• DUPlication (SVTYPE=DUP)
• Total variants (SVTYPE=DEL + SVTYPE=DUP)

Variants are only counted if the sample has a non-reference genotype (0/1 or 1/1).

References

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