Metrics Filters

Use the Metrics filters to filter data by whether variants pass filter.

Filter

Description

Small Variant QC Metrics (SNVs, MNVs, and Indels)

Filters data by Somatic Q-score, total read depth, alt allele depth, or variant read frequency.

For Tumor Normal samples, use the Tumor Normal value fields to further filter by tumor normal sample quality scores.

Copy Number Variant QC Metrics (CNVs)

Filters data by whether variants pass selected filters:

•

CLT10kb–Canvas calls with length < 10kb.

•

MaxDepth–Normal sample site depth is > 3× of the mean chromosome depth near 1 or both variant break-ends.

•

MinSomaticScore–Somatic score is < 30

•

q10–Quality < 10.

Use the Value Exceeds field to further filter by Somatic Q-score.

Structural Variant QC Metrics (SVs)

Filters data by whether variants pass selected filters:

•

MGE10kb–Manta calls with length < 10 kb.

•

MaxDepth–Normal sample site depth is > 3× mean chromosome depth near one or both variant break-ends.

•

MinSomaticScore–Somatic score is < 30.

•

MaxMQ0Frac–For a small variant (< 1000 bases), the fraction of reads in all samples with MAPQ0 around either breakend exceeds 0.4.

•

q10–Quality < 10.

Use the Value Exceeds field to further filter by Somatic Q-score, paired reads, or end reads.

For tumor samples, use the Tumor sample value fields to further filter by tumor quality scores.