Man pages for jmonlong/sveval
SV evaluation
| aldist | Align sequences and compute edit distance |
| annotateOl | Annotate the overlap between SVs |
| annotateOl.bipartite | Annotate the overlap between SVs using reciprocal overlap and... |
| annotateOl.coverage | Annotate the overlap between SVs using the reciprocal... |
| annotateOl.reciprocal | Annotate the overlap between SVs using the reciprocal overlap... |
| clusterSVs | Cluster SVs based on overlap/similarity |
| countAlleles | Count alleles in SV sites across samples |
| evalOl | Compute FP, FN, TP |
| explore_eval_svs | Interactive exploration of FP/FN/TP SVs |
| extendSVwithSimpRep | Extend SV coordinates using simple repeat annotation |
| filterSVs | Filter SVs for size and regions of interest |
| findNocalls | Find no-calls variants |
| freqAnnotate | Annotate SVs with frequency in catalog |
| ivg_sv | Interactive exploration of SVs in a variation graph |
| merge_ac_svsites_cpp | Count alleles in SV sites across samples |
| merge_gq_svsites_cpp | Genotype quality in SV sites across samples |
| mergeHets | Merge heterozygous variants |
| plot_perregion | Recall, precision, F1 per region |
| plot_persize | Recall, precision, F1 per SV size |
| plot_prcurve | Create precision-recall graphs |
| plot_ranges | Plot variants in a region |
| prepareOl | Prepare SV overlaps before annotation |
| prf | Compute precision, recall and F1 score |
| readSVvcf | Read SVs from a VCF file |
| readSVvcf.multisamps | Read SVs from a VCF file |
| read_vcf_cpp | Read VCF using CPP reader |
| read_vcf_multisamps_cpp | Read VCF using CPP reader |
| rmskAnnotate | Annotate REF/ALT sequence with RepeatMasker |
| stitchMergeHets | Stitch and merge heterozygous SVs |
| stitchSVs | Stitch fragmented SVs |
| subset_eval | Compute evaluation results on a subset of the calls |
| svevalOl | SV evaluation based on overlap and variant size |
| sveval-package | SV evaluation |
| svOverlap | Overlap SVs |
| wrapper | Wrapper function to use sveval as a command line tool |
| wrapper_mergetsvs | Internal wrapper function to merge TSVs as a command line... |
| wrapper_sveval | Internal wrapper function to run sveval as a command line... |
