diff --git a/Modules/SV/leviathan.md b/Modules/SV/leviathan.md index 9ad86ed2a..94133bdf4 100644 --- a/Modules/SV/leviathan.md +++ b/Modules/SV/leviathan.md @@ -68,6 +68,9 @@ In addition to the [!badge variant="info" corners="pill" text="common runtime op | `INPUTS` | | file/directory paths | | **yes** | Files or directories containing [input BAM files](/commonoptions.md#input-arguments) | | `--extra-params` | `-x` | string | | no | Additional naibr arguments, in quotes | | `--genome` | `-g` | file path | | yes | Genome assembly that was used to create alignments | +| `--iterations` | `-i` | integer | 50 | no | Number of iterations to perform through index (reduces memory) | +| `--min-barcodes` | `-b` | integer | 2 | no | Minimum number of barcode overlaps supporting candidate SV | +| `--min-sv` | `-m` | integer | 1000 | no | Minimum size of SV to detect | | `--populations` | `-p` | file path | | no | Tab-delimited file of sample\<*tab*\>group | ### Single-sample variant calling diff --git a/Modules/SV/naibr.md b/Modules/SV/naibr.md index 08ddf77d0..5ea97ae78 100644 --- a/Modules/SV/naibr.md +++ b/Modules/SV/naibr.md @@ -68,6 +68,8 @@ In addition to the [!badge variant="info" corners="pill" text="common runtime op | `INPUTS` | | file/directory paths | | **yes** | Files or directories containing [input BAM files](/commonoptions.md#input-arguments) | | `--extra-params` | `-x` | string | | no | Additional naibr arguments, in quotes | | `--genome` | `-g` | file path | | **yes** | Genome assembly for phasing bam files | +| `--min-barcodes` | `-b` | integer | 2 | no | Minimum number of barcode overlaps supporting candidate SV | +| `--min-sv` | `-n` | integer | 1000 | no | Minimum size of SV to detect | | `--molecule-distance` | `-m` | integer | 100000 | no | Base-pair distance threshold to separate molecules | | `--populations` | `-p` | file path | | no | Tab-delimited file of sample\<*tab*\>group | | `--vcf` | `-v` | file path | | **conditionally** | Phased vcf file for phasing bam files |