.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.3.
.TH CUTESV "1" "July 2021" "cuteSV 1.0.11" "User Commands"
.SH NAME
cuteSV \- prediction of structural variants from sequence alignments
.SH DESCRIPTION
usage: cuteSV [\-h] [\-\-version] [\-t THREADS] [\-b BATCHES] [\-S SAMPLE]
.IP
[\-\-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
.PP
                
.IP
Current version: v1.0.11
Author: Tao Jiang
Contact: tjiang@hit.edu.cn
.IP
If you use cuteSV in your work, please cite:
.IP
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
.IP
Suggestions:
.IP
For PacBio CLR data:
.TP
\fB\-\-max_cluster_bias_INS\fR
100
.TP
\fB\-\-diff_ratio_merging_INS\fR
0.3
.TP
\fB\-\-max_cluster_bias_DEL\fR
200
.TP
\fB\-\-diff_ratio_merging_DEL\fR
0.5
.IP
For PacBio CCS(HIFI) data:
.TP
\fB\-\-max_cluster_bias_INS\fR
1000
.TP
\fB\-\-diff_ratio_merging_INS\fR
0.9
.TP
\fB\-\-max_cluster_bias_DEL\fR
1000
.TP
\fB\-\-diff_ratio_merging_DEL\fR
0.5
.IP
For ONT data:
.TP
\fB\-\-max_cluster_bias_INS\fR
100
.TP
\fB\-\-diff_ratio_merging_INS\fR
0.3
.TP
\fB\-\-max_cluster_bias_DEL\fR
100
.TP
\fB\-\-diff_ratio_merging_DEL\fR
0.3
.PP
        
.SS "positional arguments:"
.TP
[BAM]
Sorted .bam file form NGMLR or Minimap2.
.TP
reference
The reference genome in fasta format.
.TP
output
Output VCF format file.
.TP
work_dir
Work\-directory for distributed jobs
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR, \fB\-v\fR
show program's version number and exit
.TP
\fB\-t\fR THREADS, \fB\-\-threads\fR THREADS
Number of threads to use.[16]
.TP
\fB\-b\fR BATCHES, \fB\-\-batches\fR BATCHES
Batch of genome segmentation interval.[10000000]
.TP
\fB\-S\fR SAMPLE, \fB\-\-sample\fR SAMPLE
Sample name/id
.TP
\fB\-\-retain_work_dir\fR
Enable to retain temporary folder and files.
.TP
\fB\-\-report_readid\fR
Enable to report supporting read ids for each SV.
.SS "Collection of SV signatures:"
.TP
\fB\-p\fR MAX_SPLIT_PARTS, \fB\-\-max_split_parts\fR MAX_SPLIT_PARTS
Maximum number of split segments a read may be aligned
before it is ignored. All split segments are
considered when using \fB\-1\fR. (Recommand \fB\-1\fR when applying
assembly\-based alignment.)[7]
.TP
\fB\-q\fR MIN_MAPQ, \fB\-\-min_mapq\fR MIN_MAPQ
Minimum mapping quality value of alignment to be taken
into account.[20]
.TP
\fB\-r\fR MIN_READ_LEN, \fB\-\-min_read_len\fR MIN_READ_LEN
Ignores reads that only report alignments with not
longer than bp.[500]
.TP
\fB\-md\fR MERGE_DEL_THRESHOLD, \fB\-\-merge_del_threshold\fR MERGE_DEL_THRESHOLD
Maximum distance of deletion signals to be merged. In
our paper, I used \fB\-md\fR 500 to process HG002 real human
sample data.[0]
.TP
\fB\-mi\fR MERGE_INS_THRESHOLD, \fB\-\-merge_ins_threshold\fR MERGE_INS_THRESHOLD
Maximum distance of insertion signals to be merged. In
our paper, I used \fB\-mi\fR 500 to process HG002 real human
sample data.[100]
.SS "Generation of SV clusters:"
.TP
\fB\-s\fR MIN_SUPPORT, \fB\-\-min_support\fR MIN_SUPPORT
Minimum number of reads that support a SV to be
reported.[10]
.TP
\fB\-l\fR MIN_SIZE, \fB\-\-min_size\fR MIN_SIZE
Minimum size of SV to be reported.[30]
.TP
\fB\-L\fR MAX_SIZE, \fB\-\-max_size\fR MAX_SIZE
Maximum size of SV to be reported.[100000]
.TP
\fB\-sl\fR MIN_SIGLENGTH, \fB\-\-min_siglength\fR MIN_SIGLENGTH
Minimum length of SV signal to be extracted.[10]
.SS "Computing genotypes:"
.TP
\fB\-\-genotype\fR
Enable to generate genotypes.
.TP
\fB\-\-gt_round\fR GT_ROUND
Maximum round of iteration for alignments searching if
perform genotyping.[500]
.SS "Force calling:"
.TP
\fB\-Ivcf\fR IVCF
Optional given vcf file. Enable to perform force
calling. [NULL]
.SS "Advanced:"
.TP
\fB\-\-max_cluster_bias_INS\fR MAX_CLUSTER_BIAS_INS
Maximum distance to cluster read together for
insertion.[100]
.TP
\fB\-\-diff_ratio_merging_INS\fR DIFF_RATIO_MERGING_INS
Do not merge breakpoints with basepair identity more
than [0.3] for insertion.
.TP
\fB\-\-max_cluster_bias_DEL\fR MAX_CLUSTER_BIAS_DEL
Maximum distance to cluster read together for
deletion.[200]
.TP
\fB\-\-diff_ratio_merging_DEL\fR DIFF_RATIO_MERGING_DEL
Do not merge breakpoints with basepair identity more
than [0.5] for deletion.
.TP
\fB\-\-max_cluster_bias_INV\fR MAX_CLUSTER_BIAS_INV
Maximum distance to cluster read together for
inversion.[500]
.TP
\fB\-\-max_cluster_bias_DUP\fR MAX_CLUSTER_BIAS_DUP
Maximum distance to cluster read together for
duplication.[500]
.TP
\fB\-\-max_cluster_bias_TRA\fR MAX_CLUSTER_BIAS_TRA
Maximum distance to cluster read together for
translocation.[50]
.TP
\fB\-\-diff_ratio_filtering_TRA\fR DIFF_RATIO_FILTERING_TRA
Filter breakpoints with basepair identity less than
[0.6] for translocation.