VCF FILTER Fields
Germline
The following table lists the VCF FILTER fields applied to germline VCF output.
|
ID |
Level |
Description |
|---|---|---|
|
MinQUAL |
Record |
QUAL score is less than 20 (not applied to records with KnownSVScoring flag) |
|
MinGQ |
Sample |
GQ score is less than 15 (filter applied at sample level; not applied to records with KnownSVScoring flag) |
|
Ploidy |
Record |
For DEL & DUP variants, the genotypes of overlapping variants (with similar size) are inconsistent with diploid expectation (not applied to records with KnownSVScoring flag) |
|
MaxDepth |
Record |
Depth is greater than 3x the median chromosome depth near one or both variant breakends (not applied to records with KnownSVScoring flag) |
|
MaxMQ0Frac |
Record |
For a small variant (<1000 bases), the fraction of reads in all samples with MAPQ0 around either breakend exceeds 0.4 (not applied to records with KnownSVScoring flag) |
|
NoPairSupport |
Record |
For variants significantly larger than the paired read fragment size, no paired reads support the alternate allele in any sample (not applied to records with KnownSVScoring flag) |
|
SampleFT |
Record |
No sample passes all the sample-level filters |
|
HomRef |
Sample |
Homozygous reference call |
Tumor-Normal Somatic
The following table lists the VCF FILTER fields applied to tumor-normal somatic VCF output.
|
ID |
Level |
Description |
|---|---|---|
|
MinSomaticScore |
Record |
SOMATICSCORE is less than 30 |
|
MaxDepth |
Record |
Normal sample site depth is greater than 3x the median chromosome depth near one or both variant breakends (not applied to records with KnownSVScoring flag) |
|
MaxMQ0Frac |
Record |
For a small variant (< 1000 bases) in the normal sample, the fraction of reads with MAPQ0 around either breakend exceeds 0.4 (not applied to records with KnownSVScoring flag) |
Tumor-Only
The following table lists the VCF FILTER fields applied to tumor-only VCF output.
|
ID |
Level |
Description |
|---|---|---|
|
MaxDepth |
Record |
Depth is greater than 3x the median chromosome depth near one or both variant breakends (not applied to records with KnownSVScoring flag) |
|
MaxMQ0Frac |
Record |
For a small variant (<1000 bases), the fraction of reads in all samples with MAPQ0 around either breakend exceeds 0.4 (not applied to records with KnownSVScoring flag) |