Package: cuteFC
cuteFCGetting Start__________    ___________      
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|_______|  |_______|     |_____|   \______/   |__|          |__________|Installation$ git clone https://github.com/tjiangHIT/cuteFC.git && cd cuteFC/ && python setup.py installIntroductionAccurate 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 examplehere.BTW, the whole functions in cuteFC have been integrated into our previous SV detector,cuteSVDependence1. python3
2. pysam
3. Biopython
4. cigar
5. numpy
6. pyvcfUsagecuteFC <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	0.5ParameterDescriptionDefault--threadsNumber of threads to use.16--batchesBatch of genome segmentation interval.10,000,000--sampleSample name/idNULL--retain_work_dirEnable to retain temporary folder and files.False--write_old_sigsEnable to output temporary sig files.False--report_readidEnable to report supporting read ids for each SV.False--max_split_partsMaximum 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_mapqMinimum mapping quality value of alignment to be taken into account.10--min_read_lenIgnores reads that only report alignments with not longer than bp.500--merge_del_thresholdMaximum distance of deletion signals to be merged.0--merge_ins_thresholdMaximum distance of insertion signals to be merged.100--min_supportMinimum number of reads that support a SV to be reported.10--min_sizeMinimum length of SV to be reported.30--max_sizeMaximum size of SV to be reported. Full length SVs are reported when using -1.100000--genotypeEnable to generate genotypes.False--gt_roundMaximum round of iteration for alignments searching if perform genotyping.500--read_rangeThe interval range for counting reads distribution.1000-IvcfOptional given vcf file. Enable to perform force calling.NULL--max_cluster_bias_INSMaximum distance to cluster read together for insertion.100--diff_ratio_merging_INSDo not merge breakpoints with basepair identity more than the ratio ofdefaultfor insertion.0.3--max_cluster_bias_DELMaximum distance to cluster read together for deletion.200--diff_ratio_merging_DELDo not merge breakpoints with basepair identity more than the ratio ofdefaultfor deletion.0.5--max_cluster_bias_INVMaximum distance to cluster read together for inversion.500--max_cluster_bias_DUPMaximum distance to cluster read together for duplication.500--max_cluster_bias_TRAMaximum distance to cluster read together for translocation.50--diff_ratio_filtering_TRAFilter breakpoints with basepair identity less than the ratio ofdefaultfor translocation.0.6--remain_reads_ratioThe 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_bedOptional given bed file. Only detect SVs in regions in the BED file.NULLCitationCao S et al. Re-genotyping structural variants through an accurate force-calling method. bioRxiv 2022.08.29.505534; doi:https://doi.org/10.1101/2022.08.29.505534ContactFor advising, bug reporting, and requiring help, please post onGithub Issueor contacttjiang@hit.edu.cn.