SvFilterAnnotations (2023_03-63-gec44de43)
Filter a structural variant list in BEDPE format based on variant annotations.
The filter definition file lists one filter per line using the following syntax:
name[tab]param1=value[tab]param2=value...
The order in the filter definition file defines the order in which the filters are applied.
Several of the filters offer more than one action:
FILTER - Remove variants if they do not match the filter.
REMOVE - Remove variants if they match the filter.
KEEP - Force variants to be kept, even if filtered out by previous filter steps.
The following filters are supported:
SV CNV overlap Filter the removes DEL/DUP without support from CNV calling.
Parameters:
min_ol - Minimum CNV overlap. [default=0.5] [min=0.0] [max=1.0]
min_size - Minimum SV size in bases. [default=10000] [min=0]
SV OMIM genes Filter for OMIM genes i.e. the 'OMIM' column is not empty.
Parameters:
action - Action to perform [default=FILTER] [valid=REMOVE,FILTER]
SV PE read depth Show only SVs with at least a certain number of Paired End Reads
(In trio/multi sample all (affected) samples must meet the requirements.)
Parameters:
PE Read Depth - minimal number of Paired End Reads [default=0] [min=0]
only_affected - Apply filter only to affected Samples. [default=false]
SV SomaticScore Show only SVs with at least a certain Somaticscore
Parameters:
Somaticscore - min. Somaticscore [default=0] [min=0]
SV allele frequency NGSD Filter based on the allele frequency of this structural variant in the NGSD.
Note: this filter should only be used for whole genome samples.
Parameters:
max_af - Maximum allele frequency in % [default=1] [min=0.0] [max=200.0]
SV break point density NGSD Filter based on the density of SV break points in the NGSD in the CI of the structural variant.
Parameters:
max_density - Maximum density in the confidence interval of the SV [default=20] [min=0]
remove_strict - Remove also SVs in which only one break point is above threshold. [default=false]
SV compound-heterozygous Filter for compound-heterozygous SVs.
Mode 'SV-SV' detects genes with two or more SV hits.
Mode 'SV-SNV/INDEL' detectes genes with exactly one SV and exactly one small variant hit (after other filters are applied).
Parameters:
mode - Compound-heterozygotes detection mode. [default=n/a] [valid=n/a,SV-SV,SV-SNV/INDEL]
SV count NGSD Filter based on the hom/het occurances of a structural variant in the NGSD.
Parameters:
max_count - Maximum NGSD SV count [default=20] [min=0]
ignore_genotype - If set, all NGSD entries are counted independent of the variant genotype. Otherwise, for homozygous variants only homozygous NGSD entries are counted and for heterozygous variants all NGSD entries are counted. [default=false]
SV filter columns Filter structural variants based on the entries of the 'FILTER' column.
Parameters:
entries - Filter column entries [non-empty]
action - Action to perform [default=REMOVE] [valid=REMOVE,FILTER,KEEP]
SV gene constraint Filter based on gene constraint (gnomAD o/e score for LOF variants).
Note that gene constraint is most helpful for early-onset severe diseases.
For details on gnomAD o/e, see https://macarthurlab.org/2018/10/17/gnomad-v2-1/
Parameters:
max_oe_lof - Maximum gnomAD o/e score for LoF variants [default=0.35] [min=0.0] [max=1.0]
SV gene overlap Filter based on gene overlap.
Parameters:
complete - Overlaps the complete gene. [default=true]
exonic/splicing - Overlaps the coding or splicing region of the gene. [default=true]
intronic/intergenic - Overlaps the intronic/intergenic region of the gene only. [default=false]
SV genotype affected Filter structural variants (of affected samples) based on their genotype.
Parameters:
genotypes - Structural variant genotype(s) [valid=wt,het,hom,n/a] [non-empty]
same_genotype - Also check that all 'control' samples have the same genotype. [default=false]
SV genotype control Filter structural variants of control samples based on their genotype.
Parameters:
genotypes - Structural variant genotype(s) [valid=wt,het,hom,n/a] [non-empty]
same_genotype - Also check that all 'control' samples have the same genotype. [default=false]
SV paired read AF Show only SVs with a certain Paired Read Allele Frequency +/- 10%
(In trio/multi sample all (affected) samples must meet the requirements.)
Parameters:
Paired Read AF - Paired Read Allele Frequency +/- 10% [default=0] [min=0.0] [max=1.0]
only_affected - Apply filter only to affected Samples. [default=false]
SV quality Filter structural variants based on their quality.
Parameters:
quality - Minimum quality score [default=0] [min=0]
SV remove chr type Removes all structural variants which contains non-standard/standard chromosomes.
Parameters:
chromosome type - Structural variants containing non-standard/standard chromosome are removed. [default=special chromosomes] [valid=special chromosomes,standard chromosomes] [non-empty]
SV size Filter for SV size in the given range.
Parameters:
min_size - Minimum SV size (absolute size). [default=0] [min=0]
max_size - Maximum SV size (absolute size). Select 0 for infinity. [default=0] [min=0]
SV split read AF Show only SVs with a certain Split Read Allele Frequency +/- 10%
(In trio/multi sample all (affected) samples must meet the requirements.)
Parameters:
Split Read AF - Split Read Allele Frequency +/- 10% [default=0] [min=0.0] [max=1.0]
only_affected - Apply filter only to affected Samples. [default=false]
SV trio Filter trio structural variants
Parameters:
types - Variant types [default=de-novo,recessive,comp-het,LOH,x-linked] [valid=de-novo,recessive,comp-het,LOH,x-linked,imprinting]
gender_child - Gender of the child - if 'n/a', the gender from the GSvar file header is taken [default=n/a] [valid=male,female,n/a]
build - Genome build used for pseudoautosomal region coordinates [default=hg19] [valid=hg19,hg38]
SV type Filter based on SV types.
Parameters:
Structural variant type - Structural variant type [valid=DEL,DUP,INS,INV,BND] [non-empty]
Mandatory parameters:
-in <file> Input structural variant list in BEDPE format.
-out <file> Output structural variant list in BEDPE format.
-filters <file> Filter definition file.
Special parameters:
--help Shows this help and exits.
--version Prints version and exits.
--changelog Prints changeloge and exits.
--tdx Writes a Tool Definition Xml file. The file name is the application name with the suffix '.tdx'.
SvFilterAnnotations 2023_03-63-gec44de43
2020-04-16 Initial version of the tool. Based on VariantFilterAnnotations.