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SvFilterAnnotations tool help

SvFilterAnnotations (2024_02-126-g4f44d5e5)

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]
                              only_system_specific - Filter only based on the density of breakpoint of the current processing system. [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/near gene - Overlaps the intronic region or less than 5kb up/down stream of the gene . [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]
SV-lr AF                    Show only (lr) SVs with a allele frequency between the given interval
                            Parameters:
                              min_af - minimal allele frequency [default=0] [min=0.0] [max=1.0]
                              max_af - maximal allele frequency [default=1] [min=0.0] [max=1.0]
SV-lr support reads         Show only (lr) SVs with a minimum number of supporting reads
                            Parameters:
                              min_support - Minimum support read count [default=5] [min=0] [max=10000]

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 changelog

SvFilterAnnotations 2024_02-126-g4f44d5e5

2020-04-16 Initial version of the tool. Based on VariantFilterAnnotations.

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