cuteSV1

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.