CUTESV(1)

👑 cuteSV, section 1, user commands 👑

okay so hi bestie 💖 you just opened the manual page for cuteSV, and it lives in section 1 (User Commands). It's literally the cutest little structural-variant caller and I'm obsessed. Buckle up, we're going through every single flag together, no skipping, periodt. 🎀

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🌸 NAME 🌸

cuteSV — prediction of structural variants from sequence alignments ✨

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🦋 DESCRIPTION 🦋

here's the usage, copy-pasted with love and zero edits, so you can see exactly how the vibe starts:

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 (yes bestie, cite it, it's the rules 🫶):

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

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💡 Suggestions (the tuning cheat sheet) 💡

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

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🎀 positional arguments 🎀

these are the four things you literally have to hand over, no cap:

• [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

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🧚 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.

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🔥 Collection of SV signatures 🔥

the "what even counts as a signal" section:

• -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]

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💅 Generation of SV clusters 💅

where the little signals get to hold hands and become an actual SV:

• -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]

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🧬 Computing genotypes 🧬

• --genotype — Enable to generate genotypes.
• --gt_round GT_ROUND — Maximum round of iteration for alignments searching if perform genotyping. [500]

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💀 Force calling 💀

• -Ivcf IVCF — Optional given vcf file. Enable to perform force calling. [NULL]

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🌟 Advanced 🌟

the deep-magic knobs, iykyk:

• --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.

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that's the whole page, bestie — go call some SVs 💖✨🦋

this was cuteSV 1.0.11, dated July 2021. mwah, go be a main character in your own terminal 🎀👑