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 |
|---|---|---|---|---|---|---|---|---|
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_v3.0.0_systematic_noise.sv.bedpe.gz | can be used for FF, FFPE |
WGS | TruSeq PCR Free | 100 | 1kg cell lines | 30x | WGS_hg19_v3.0.0_systematic_noise.sv.bedpe.gz | can be used for FF, FFPE |
WGS | TruSeq PCR Free | 100 | 1kg cell lines | 30x | WGS_hs37d5_v3.0.0_systematic_noise.sv.bedpe.gz | can be used for FF, FFPE |
WGS | IDPF | 46 | PBMC, BMA | 200x | IDPF_WGS_hg38_v3.0.0_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 |
|---|---|---|---|---|---|---|---|---|
v3.0.0 | ||||||||
v2.0.0 | ||||||||
v1.0.0 |
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