Noise Baselines

SNV Systematic Noise Files

In somatic variant calling mode, systematic noise filter can be used to remove systematic noise observed in normal samples. Using this filter is essential for tumor-only and is recommended for tumor-normal mode. A systematic noise file can be generated by running the somatic TO pipeline on normal samples. We recommend using a systematic noise file based on normal samples that match the library prep of the tumor samples. For more details please look at DRAGEN Variant Calling user guide Alternately, a set of prebuilt SNV systematic noise BED files can be downloaded from the DRAGEN Software Support Site page

Assay	Library Prep	#Samples	Sample type	Coverage	Systematic Noise File Name	Comments
WGS	mixed	40	FF	70x	WGS_hg38_v2.0.0_systematic_noise.snv.bed.gz	can be used for FF
WGS	IDPF	46	PBMC,BMA	200x	IDPF_WGS_hg38_v.2.0.0_systematic_noise.snv.bed.gz	can be used for heme
WGS	TruSeq PCR	42	FFPE	100x	FFPE_WGS_hg38_v2.0.0_systematic_noise.snv.bed.gz	can be used for FFPE
WES	mixed	60	mix FF & FFPE	100x	WES_hg38_v2.0.0_systematic_noise.snv.bed.gz	can be used for FF, FFPE

SNV Systematic Noise File Compatibility

Below is the table summarizing the compatibility of different SNV baseline noise versions and different DRAGEN major versions (from DRAGEN 3.7 to DRAGEN 4.3).

SNV Systematic Noise Version	3.7	3.8	3.9	3.10	4.0	4.1	4.2	4.3	4.4
v2.0.0								✔️	✔️
v1.1.0							✔️
v1.0.0	✔️	✔️	✔️	✔️	✔️	✔️

SV Systematic Noise Files

When DRAGEN-SV is used in the somatic mode (tumor-only or tumor-normal), a BEDPE file with a set of paired-end regions in the BEDPE file format can be specified to filter out sequencing/systematic noise and also recurrent germline calls. The systematic noise BEDPE file is built using VCFs that were generated by the DRAGEN-SV tumor-only pipeline when run on normal samples that do not necessarily match to the subject the tumor sample was taken from. The file might contain several dozen samples. For more details please look at DRAGEN SV user guide. A set of prebuilt SV systematic noise BEDPE files can be downloaded from the DRAGEN Software Support Site page

Assay	Library Prep	#Samples	Sample type	Coverage	Systematic Noise File Name	Comments
WGS	TruSeq PCR Free	100	1kg cell lines	30x	WGS_hg38_v3.1.0_systematic_noise.sv.bedpe.gz	can be used for FF, FFPE
WGS	TruSeq PCR Free	100	1kg cell lines	30x	WGS_hg19_v3.1.0_systematic_noise.sv.bedpe.gz	can be used for FF, FFPE
WGS	TruSeq PCR Free	100	1kg cell lines	30x	WGS_hs37d5_v3.1.0_systematic_noise.sv.bedpe.gz	can be used for FF, FFPE
WGS	IDPF	46	PBMC, BMA	200x	WGS_FF_Heme_hg38_v3.1.0_systematic_noise.sv.bedpe.gz	can be used for heme
WGS	IDPF	46	PBMC, BMA	200x	WGS_FF_Heme_hg19_v3.1.0_systematic_noise.sv.bedpe.gz	can be used for heme
WGS	IDPF	46	PBMC, BMA	200x	WGS_FF_Heme_hghs37d5_chr_v3.1.0_systematic_noise.sv.bedpe.gz	can be used for heme
WES/panels					untested

SV Systematic Noise File Compatibility

Below is the table summarizing the compatibility of different SV baseline noise versions and different DRAGEN major versions (from DRAGEN 3.7 to DRAGEN 4.3).

SV Systematic Noise Version	3.7	3.8	3.9	3.10	4.0	4.1	4.2	4.3	4.4
v3.1.0									✔️
v3.0.0								✔️
v2.0.0							✔️
v1.0.0					✔️	✔️