CUTESV(1) User Commands CUTESV(1)

cuteSV - prediction of structural variants from sequence alignments

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:
100
0.3
200
0.5
For PacBio CCS(HIFI) data:
1000
0.9
1000
0.5
For ONT data:
100
0.3
100
0.3

[BAM]
Sorted .bam file form NGMLR or Minimap2.
The reference genome in fasta format.
Output VCF format file.
Work-directory for distributed jobs

show this help message and exit
show program's version number and exit
Number of threads to use.[16]
Batch of genome segmentation interval.[10000000]
Sample name/id
Enable to retain temporary folder and files.
Enable to report supporting read ids for each SV.

Maximum number of split segments a read may be aligned before it is ignored. All split segments are considered when using -1. (Recommand -1 when applying assembly-based alignment.)[7]
Minimum mapping quality value of alignment to be taken into account.[20]
Ignores reads that only report alignments with not longer than bp.[500]
Maximum distance of deletion signals to be merged. In our paper, I used -md 500 to process HG002 real human sample data.[0]
Maximum distance of insertion signals to be merged. In our paper, I used -mi 500 to process HG002 real human sample data.[100]

Minimum number of reads that support a SV to be reported.[10]
Minimum size of SV to be reported.[30]
Maximum size of SV to be reported.[100000]
Minimum length of SV signal to be extracted.[10]

Enable to generate genotypes.
Maximum round of iteration for alignments searching if perform genotyping.[500]

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

Maximum distance to cluster read together for insertion.[100]
Do not merge breakpoints with basepair identity more than [0.3] for insertion.
Maximum distance to cluster read together for deletion.[200]
Do not merge breakpoints with basepair identity more than [0.5] for deletion.
Maximum distance to cluster read together for inversion.[500]
Maximum distance to cluster read together for duplication.[500]
Maximum distance to cluster read together for translocation.[50]
Filter breakpoints with basepair identity less than [0.6] for translocation.
July 2021 cuteSV 1.0.11