cuteSV-v1.0.9

cutesv (v1.0.9):

1. Change 0-based pos into 1-based pos in DUP in order to support bcftools conversion.
2. Correct REF and ALT fields. Adjust END value of INS to make it equal to the value of POS.
3. Improve the description of errors.
4. Add usegalaxy.eu badge.
5. Remove CHR2 and the corresponding END position on the BND call.
6. Skip generating empty signature file and rewrite the job schedule.
7. Add force calling function and enable cuteSV to perform population-based SV calling.
8. Fix several minor bugs.

cuteSV-v1.0.8

cutesv (v1.0.8):

1. Rewirte the function of ins/del signatures clustering.
2. Update the recommandation parameters for different sequencing datasets.
3. Replace <DEL>/<INS> with its variant allele sequence, which needs the reference genome sequence as input.
4. Fix several bugs.

cuteSV-v1.0.7

1. Add read name list for each SV call.
2. Fix several descriptions in VCF header field.

cuteSV-v1.0.6

1.Improvement of genotyping by calculation of likelihood.
2.Add variant quality value, phred-scaled genotype likelihood and genotype quality in order to filter false positive SV or quality control.
3.Add --gt_round parameter to control the number of read scans.
4.Add variant strand of DEL/DUP/INV.
5.Fix several bugs.

cuteSV-v1.0.5

cuteSV (v1.0.5):
1.Add new options for specificly setting the threshold of deletion/insertion signals merging in the same read. The default parameters are 0 bp for deletion and 100 bp for insertion.
2.Remove parameter --merge_threshold.
3.Fix bugs in inversion and translocation calling.
4.Add new option for specificly setting the maximum size of SV to be discovered. The default value is 100,000 bp.

cuteSV-v1.0.4

1.Add a new option for specificly setting the threshold of SV signals merging in the same read. The default parameter is 500 bp. You can reduce it for high-quality sequencing datasets like PacBio HiFi (CCS).
2.Make the genotyping function optional.
3.Enable users to set the threshold of SV allele frequency of homozygous/heterozygous.
4.Update the description of recommendation parameters in processing ONT data.

cuteSV-v1.0.3

1.Refine the genotyping model.
2.Adjust the threshold value of heterozygosis alleles.

cuteSV-v1.0.2

1.Improve the genotyping performance and enable it to be default option.
2.Make the description of parameters better.
3.Modify the header description of vcf file.
4.Add two new indicators, i.e., BREAKPOINT_STD and SVLEN_STD, to further characterise deletion and insertion.
5.Remove a few redundant functions which will reduce code readability.

cuteSV-v1.0.1

delete out of date files