---
name: "cuteSV"
section: "1"
platform: "linux"
package: "cutesv"
version: "2.1.1-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/cuteSV"
---

# cuteSV(1)

prediction of structural variants from sequence alignments

## NAME

cuteSV - prediction of structural variants from sequence alignments

## DESCRIPTION

usage: cuteSV \[-h\] \[--version\] \[-t THREADS\] \[-b BATCHES\] \[-S SAMPLE\]

-

  \[--retain\_work\_dir\] \[--report\_readid\] \[-p MAX\_SPLIT\_PARTS\] \[-q MIN\_MAPQ\] \[-r MIN\_READ\_LEN\] \[-md MERGE\_DEL\_THRESHOLD\] \[-mi MERGE\_INS\_THRESHOLD\] \[-s MIN\_SUPPORT\] \[-l MIN\_SIZE\] \[-L MAX\_SIZE\] \[-sl MIN\_SIGLENGTH\] \[--genotype\] \[--gt\_round GT\_ROUND\] \[-Ivcf IVCF\] \[--max\_cluster\_bias\_INS MAX\_CLUSTER\_BIAS\_INS\] \[--diff\_ratio\_merging\_INS DIFF\_RATIO\_MERGING\_INS\] \[--max\_cluster\_bias\_DEL MAX\_CLUSTER\_BIAS\_DEL\] \[--diff\_ratio\_merging\_DEL DIFF\_RATIO\_MERGING\_DEL\] \[--max\_cluster\_bias\_INV MAX\_CLUSTER\_BIAS\_INV\] \[--max\_cluster\_bias\_DUP MAX\_CLUSTER\_BIAS\_DUP\] \[--max\_cluster\_bias\_TRA MAX\_CLUSTER\_BIAS\_TRA\] \[--diff\_ratio\_filtering\_TRA DIFF\_RATIO\_FILTERING\_TRA\] \[BAM\] reference output work\_dir

-

  Current version: v1.0.11 Author: Tao Jiang Contact: tjiang@hit.edu.cn

-

  If you use cuteSV in your work, please cite:

-

  Jiang T et al. Long-read-based human genomic structural variation detection with cuteSV. Genome Biol 21,189(2020). https://doi.org/10.1186/s13059-020-02107-y

-

  Suggestions:

-

  For PacBio CLR data:

- **--max\_cluster\_bias\_INS**

  100

- **--diff\_ratio\_merging\_INS**

  0\.3

- **--max\_cluster\_bias\_DEL**

  200

- **--diff\_ratio\_merging\_DEL**

  0\.5

-

  For PacBio CCS(HIFI) data:

- **--max\_cluster\_bias\_INS**

  1000

- **--diff\_ratio\_merging\_INS**

  0\.9

- **--max\_cluster\_bias\_DEL**

  1000

- **--diff\_ratio\_merging\_DEL**

  0\.5

-

  For ONT data:

- **--max\_cluster\_bias\_INS**

  100

- **--diff\_ratio\_merging\_INS**

  0\.3

- **--max\_cluster\_bias\_DEL**

  100

- **--diff\_ratio\_merging\_DEL**

  0\.3

### positional arguments:

- \[BAM\]

  Sorted .bam file form NGMLR or Minimap2.

- reference

  The reference genome in fasta format.

- output

  Output VCF format file.

- work\_dir

  Work-directory for distributed jobs

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **--version**, **-v**

  show program's version number and exit

- **-t** THREADS, **--threads** THREADS

  Number of threads to use.\[16\]

- **-b** BATCHES, **--batches** BATCHES

  Batch of genome segmentation interval.\[10000000\]

- **-S** SAMPLE, **--sample** SAMPLE

  Sample name/id

- **--retain\_work\_dir**

  Enable to retain temporary folder and files.

- **--report\_readid**

  Enable to report supporting read ids for each SV.

### Collection of SV signatures:

- **-p** MAX\_SPLIT\_PARTS, **--max\_split\_parts** MAX\_SPLIT\_PARTS

  Maximum number of split segments a read may be aligned before it is ignored. All split segments are considered when using **-1**. (Recommend **-1** when applying assembly-based alignment.)\[7\]

- **-q** MIN\_MAPQ, **--min\_mapq** MIN\_MAPQ

  Minimum mapping quality value of alignment to be taken into account.\[20\]

- **-r** MIN\_READ\_LEN, **--min\_read\_len** MIN\_READ\_LEN

  Ignores reads that only report alignments with not longer than bp.\[500\]

- **-md** MERGE\_DEL\_THRESHOLD, **--merge\_del\_threshold** MERGE\_DEL\_THRESHOLD

  Maximum distance of deletion signals to be merged. In our paper, I used **-md** 500 to process HG002 real human sample data.\[0\]

- **-mi** MERGE\_INS\_THRESHOLD, **--merge\_ins\_threshold** MERGE\_INS\_THRESHOLD

  Maximum distance of insertion signals to be merged. In our paper, I used **-mi** 500 to process HG002 real human sample data.\[100\]

### Generation of SV clusters:

- **-s** MIN\_SUPPORT, **--min\_support** MIN\_SUPPORT

  Minimum number of reads that support a SV to be reported.\[10\]

- **-l** MIN\_SIZE, **--min\_size** MIN\_SIZE

  Minimum size of SV to be reported.\[30\]

- **-L** MAX\_SIZE, **--max\_size** MAX\_SIZE

  Maximum size of SV to be reported.\[100000\]

- **-sl** MIN\_SIGLENGTH, **--min\_siglength** MIN\_SIGLENGTH

  Minimum length of SV signal to be extracted.\[10\]

### Computing genotypes:

- **--genotype**

  Enable to generate genotypes.

- **--gt\_round** GT\_ROUND

  Maximum round of iteration for alignments searching if perform genotyping.\[500\]

### Force calling:

- **-Ivcf** IVCF

  Optional given vcf file. Enable to perform force calling. \[NULL\]

### Advanced:

- **--max\_cluster\_bias\_INS** MAX\_CLUSTER\_BIAS\_INS

  Maximum distance to cluster read together for insertion.\[100\]

- **--diff\_ratio\_merging\_INS** DIFF\_RATIO\_MERGING\_INS

  Do not merge breakpoints with basepair identity more than \[0.3\] for insertion.

- **--max\_cluster\_bias\_DEL** MAX\_CLUSTER\_BIAS\_DEL

  Maximum distance to cluster read together for deletion.\[200\]

- **--diff\_ratio\_merging\_DEL** DIFF\_RATIO\_MERGING\_DEL

  Do not merge breakpoints with basepair identity more than \[0.5\] for deletion.

- **--max\_cluster\_bias\_INV** MAX\_CLUSTER\_BIAS\_INV

  Maximum distance to cluster read together for inversion.\[500\]

- **--max\_cluster\_bias\_DUP** MAX\_CLUSTER\_BIAS\_DUP

  Maximum distance to cluster read together for duplication.\[500\]

- **--max\_cluster\_bias\_TRA** MAX\_CLUSTER\_BIAS\_TRA

  Maximum distance to cluster read together for translocation.\[50\]

- **--diff\_ratio\_filtering\_TRA** DIFF\_RATIO\_FILTERING\_TRA

  Filter breakpoints with basepair identity less than \[0.6\] for translocation.