Post Somatic Calling Filtering
The following options are available for post somatic calling filtering:
|
Option |
Description |
|---|---|
|
--vc-sq-call-threshold |
Emits calls in the VCF. The default is 3.0 for tumor-normal and 0.1 for tumor-only. If the value for vc-sq-filter-threshold is lower than vc-sq-call-threshold, the filter threshold value is used instead of the call threshold value. |
|
--vc-sq-filter-threshold |
Marks emitted VCF calls as filtered. The default is 17.5 for tumor-normal and 6.5 for tumor-only. |
|
--vc-enable-triallelic-filter |
Enables the multiallelic filter. The default is true. |
|
--vc-enable-af-filter |
Enables the allele frequency filter. The default value is false. When set to true, the VCF excludes variants with allele frequencies below the AF call threshold or variants with an allele frequency below the AF filter threshold and tagged with low AF filter tag. The default AF call threshold is 1% and the default AF filter threshold is 5%. To change the threshold values, use the following command line options: vc-af-call-threshold and vc-af-filter-threshold. |
|
--vc-enable-non-homref-normal-filter |
Enables the non-homref normal filter. The default value is true. When set to true, the VCF filters out variants if the normal sample genotype is not a homozygous reference. |
|
--vc-enable-vaf-ratio-filter |
Adds one condition to be filtered out by the alt_allele_in_normal filter. The default value is false. When set to true, the VCF filters out variants if the normal sample AF is greater than 20% of tumor sample AF. |
The following table describes the available somatic calling filters.
|
Somatic Mode |
Filter ID |
Description |
|---|---|---|
|
Tumor-Only & Tumor-Normal |
clustered_events |
Clustered events were observed in a given active region. Threshold for clustered events is configurable (default is ≥ 3). Enabled only when using --vc-enable-gatk-acceleration=true. |
|
Tumor-Only & Tumor-Normal |
weak_evidence |
Variant does not meet likelihood threshold. The likelihood ratio for SQ tumor-normal is < 17.5 or < 3.0 for SQ tumor-only. |
|
Tumor-Only & Tumor-Normal |
multiallelic |
Site filtered if there are two or more alt alleles at this location in the tumor. |
|
Tumor-Only & Tumor-Normal |
str_contraction |
Suspected PCR error where the alt allele is one repeat unit less than the reference. Enabled only when using --vc-enable-gatk-acceleration=true. |
|
Tumor-Only & Tumor-Normal |
base_quality |
Median base quality of alt reads at this locus is < 20. |
|
Tumor-Only & Tumor-Normal |
mapping_quality |
Median mapping quality of alt reads at this locus is < 20 (tumor-normal) or < 30 (tumor-only). |
|
Tumor-Only & Tumor-Normal |
fragment_length |
Absolute difference between the median fragment length of alt reads and median fragment length of ref reads at a given locus > 10000. |
|
Tumor-Only & Tumor-Normal |
read_position |
Median of distances between the start and end of read and a given locus < 5 (the variant is too close to edge of all the reads). |
|
Tumor-Only & Tumor-Normal |
panel_of_normals |
Seen in at least one sample in the panel of normal VCF. |
|
Tumor-Only & Tumor-Normal |
low_af |
Allele frequency is below the threshold specified with --vc-af-filter-threshold (default is 5%). Enabled only when using --vc-enable-af-filter=true. |
|
Tumor-Only & Tumor-Normal |
systematc_noise |
If AQ score is < 10 (default) for tumor-normal or < 60 (default) for tumor-only, the site is filtered. |
|
Tumor-Only & Tumor-Normal |
low_frac_info_reads |
The fraction of informative reads is below the threshold. The default threshold value is 0.5. |
|
Tumor-Only & Tumor-Normal |
low_depth |
The site filtered because the number of reads does not meet the low_frac_info_reads threshold value. |
