De Novo Small Variant Filtering

The filtering step identifies de novo variants calls of the joint calling workflow in regions with ploidy changes. Since de novo calling can have reduced specificity in regions where at least one of the pedigree members shows non-diploid genotypes, the de novo variant filtering marks relevant variants and thus can improve specificity of the call set.

Based on the structural and copy number variant calls of the pedigree, the FORMAT/DN field in the proband is changed from the original DeNovo value to DeNovoSV or DeNovoCNV if the de novo variant overlaps with a ploidy-changing SV or CNV, respectively. All other variant details remain unchanged, and all variants of the input VCF will also be present in the filtered output VCF. Structural or copy number variants which result in no change of ploidy, such as inversions, are not considered in the filtering. As an example, a de novo SNV calls in the input VCF

chr1 234710899 . T C 44.74 PASS
AC=1;AF=0.167;AN=6;DP=73;FS=4.720;MQ=250.00;MQRankSum=5.310;QD=1.15;ReadPosRankSum=1.366;SOR=0.251
GT:AD:AF:DP:GQ:FT:F1R2:F2R1:PL:GL:GP:PP:DQ:DN
0/1:21,18:0.462:39:48:PASS:14,10:7,8:84,0,50:-8.427,0,-5:4.950e+01,7.041e-05,5.300e+01:15,0,120:3.2280e-01:DeNovo
0/0:13,0:0.000:11:30:PASS:.:.:0,30,450:.:.:10,0,227
0/0:25,0:0.000:22:60:PASS:.:.:0,60,899:.:.:0,33,227

Overlapping with an SV duplication in the proband, mother or father would be represented in the filtered output VCF as follows:

chr1 234710899 . T C 44.74 PASS
AC=1;AF=0.167;AN=6;DP=73;FS=4.720;MQ=250.00;MQRankSum=5.310;QD=1.15;ReadPosRankSum=1.366;SOR=0.251
GT:AD:AF:DP:GQ:FT:F1R2:F2R1:PL:GL:GP:PP:DQ:DN
0/1:21,18:0.462:39:48:PASS:14,10:7,8:84,0,50:-8.427,0,-5:4.950e+01,7.041e-05,5.300e+01:15,0,120:3.2280e-01:DeNovoSV
0/0:13,0:0.000:11:30:PASS:.:.:0,30,450:.:.:10,0,227
0/0:25,0:0.000:22:60:PASS:.:.:0,60,899:.:.:0,33,227

The following is an example command line for running the de novo filtering, based on the files returned by the joint calling workflows:

dragen \
--dn-enable-denovo-filtering true \
--dn-input-joint-vcf <JOINT_SMALL_VARIANT_VCF> \
--dn-output-joint-vcf <OUTPUT_VCF> \
--dn-sv-vcf <JOINT_SV_VCF> \
--dn-cnv-vcf <JOINT_CNV_VCF> \
--enable-map-align false

The following options are used for de novo variant filtering:

Option

Description

--dn-input-vcf

Joint small variant VCF from the de novo calling step to be filtered.

--dn-output-vcf

File location to which the filtered VCF should be written. If not specified, the input VCF is overwritten.

--dn-sv-vcf

Joint structural variant VCF from the SV calling step. If omitted, checks with overlapping structural variants are skipped.

--dn-cnv-vcf

Joint structural variant VCF from the CNV calling step. If omitted, checks with overlapping copy number variants are skipped.