cuteFC

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Getting Start

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|_______|  |_______|     |_____|   \______/   |__|          |__________|

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Installation

$ git clone https://github.com/Meltpinkg/cuteFC.git && cd cuteFC/ && python setup.py install 

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Introduction

Accurate genotype assignment for SVs remains challenging, especially in large-scale joint calling. We develop cuteFC to achieve accurate and efficient regenotyping of SVs through a force-calling approach. Benchmarking results demonstrated that cuteFC outperforms state-of-the-art methods with 2%~5% higher F1 scores. SV joint-calling within the cohort revealed that cuteFC constructs the higher-quality genomic atlas with minimal computational resources. These results prove cuteFC to be a scalable and robust approach suitable for clinical applications, population studies, and related fields.

For more detailed implementation of SV benchmarks, we show an example here.

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Dependence

1. python3
2. pysam
3. Biopython
4. cigar
5. numpy
6. pyvcf

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Usage

cuteFC <sorted.bam> <reference.fa> <output.vcf> <work_dir> -Ivcf <target.vcf>

Suggestions

> For PacBio CLR data:
	--max_cluster_bias_INS		500
	--diff_ratio_merging_INS	0.5
	--max_cluster_bias_DEL	1000
	--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		1000
	--diff_ratio_merging_INS	0.5
	--max_cluster_bias_DEL	1000
	--diff_ratio_merging_DEL	0.5

Parameter	Description	Default
--threads	Number of threads to use.	16
--batches	Batch of genome segmentation interval.	10,000,000
--sample	Sample name/id	NULL
--retain_work_dir	Enable to retain temporary folder and files.	False
--write_old_sigs	Enable to output temporary sig files.	False
--report_readid	Enable to report supporting read ids for each SV.	False
--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
--min_mapq	Minimum mapping quality value of alignment to be taken into account.	10
--min_read_len	Ignores reads that only report alignments with not longer than bp.	500
--merge_del_threshold	Maximum distance of deletion signals to be merged.	0
--merge_ins_threshold	Maximum distance of insertion signals to be merged.	100
--min_support	Minimum number of reads that support a SV to be reported.	10
--min_size	Minimum length of SV to be reported.	30
--max_size	Maximum size of SV to be reported. Full length SVs are reported when using -1.	100000
--genotype	Enable to generate genotypes.	False
--gt_round	Maximum round of iteration for alignments searching if perform genotyping.	500
--read_range	The interval range for counting reads distribution.	1000
--detect_large_ins	Enable the detection of large insertions.	False
--max_cluster_bias_INS	Maximum distance to cluster read together for insertion.	100
--diff_ratio_merging_INS	Do not merge breakpoints with basepair identity more than the ratio of default for insertion.	0.3
--max_cluster_bias_DEL	Maximum distance to cluster read together for deletion.	200
--diff_ratio_merging_DEL	Do not merge breakpoints with basepair identity more than the ratio of default for deletion.	0.5
--max_cluster_bias_INV	Maximum distance to cluster read together for inversion.	500
--max_cluster_bias_DUP	Maximum distance to cluster read together for duplication.	500
--max_cluster_bias_TRA	Maximum distance to cluster read together for translocation.	50
--diff_ratio_filtering_TRA	Filter breakpoints with basepair identity less than the ratio of default for translocation.	0.6
--remain_reads_ratio	The ratio of reads remained in cluster to generate the breakpoint. Set lower to get more precise breakpoint when the alignment data have high quality but recommand over 0.5.	1
-include_bed	Optional given bed file. Only detect SVs in regions in the BED file.	NULL

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Citation

Jiang, T., Cao, S., Liu, Y. et al. cuteFC: regenotyping structural variants through an accurate and efficient force-calling method. Genome Biol 26, 166 (2025). https://doi.org/10.1186/s13059-025-03642-2

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Contact

For advising, bug reporting, and requiring help, please post on Github Issue or contact tjiang@hit.edu.cn.