Systematic Noise Creation Options
The following options are available to create systematic noise BED files from normal VCF files.
|
Name |
Description |
Command Line Equivalent |
Value |
|---|---|---|---|
|
vc-systematic-noise-raw-input-list |
List of VCFs to be used. One VCF per line. |
--vc-systematic-noise-raw-input-list |
|
|
vc-systematic-noise-germline-vaf-threshold |
Minimal variant allele frequency to remove potential germlines from the systematic noise file building. If not specified, all variants are used. |
--vc-systematic-noise-germline-vaf-threshold |
0–1 |
|
vc-systematic-noise-use-germline-tag |
Whether to use DRAGEN internal germline tagging to remove potential germlines. Mutually exclusive with --vc-systematic-noise-germline-vaf-threshold . |
--vc-systematic-noise-use-germline-tag |
true/false |
|
vc-systematic-noise-method |
Method to calculate the systematic noise level across samples. |
--vc-systematic-noise-method |
mean / max / aggregate |