table of contents
CUTESV(1) | User Commands | CUTESV(1) |
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:¶
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.
July 2021 | cuteSV 1.0.11 |