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.  (Recommand  -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.