Man pages for vladimirsouza/lrRNA-seq_benchmark
Figure out how to call varaints from Iso-Seq data
| add_a_method_indel_information_to_master_table | Add column that states whether the variant called by a method... |
| add_format_tag_from_vcf | Add a FORMAT tag from a VCF file to a master table |
| add_homopolymer_length_when_indels | Add homopolymer lengths to a master table |
| add_info_tag_from_vcf | Add a INFO tag from a VCF file to a master table |
| add_method_vs_truth_comparison_to_master_table | Add classiffication of variants calls by comparing to the... |
| add_number_of_n_cigar_reads_to_master_table | Add the count of N-cigar reads to the master table |
| add_qual_from_vcf | Add QUAL from a VCF into a master table |
| add_read_coverage_from_bam_to_master_table | Add read coverage (taken from BAM file) of each dataset to a... |
| add_some_read_statistic_from_bam_metacolumn | Add some statistic of a tag about reads of a BAM file |
| add_splice_site_info_to_master_table | Add columns about spice sites to a master table |
| add_the_ground_truth_indel_information_to_master_table | Add column that states whether the variant in the... |
| add_two_method_comparison_to_master_table | Add column to compare two methods in a master table |
| add_variant_density_of_a_method | Add column of density of variants around each variant called... |
| add_variant_type_to_master_table | Add a column that states the variant type according a method... |
| calc_accuracy_measures | Calculate precision, sensitivity and F1-score of a method in... |
| calculate_precision_recall_for_coverage_ranges | Calculate accuracy measures, per read coverage ranges, for... |
| calculate_precision_recall_for_multi_master_tables | Calculate accuracy measures for multiple master tables |
| calculate_precision_recall_for_multi_master_tables2 | Calculate accuracy measures for multiple master tables and... |
| calculate_precision_recall_for_n_cigar_read_count_intervarls | For each N-cigar-read-count interval, calculate accuracy... |
| check_accuracy_per_coverage | Barplot of accuracy measures for different methods and... |
| get_splice_sites_info | Get all splice sites positions of a BAM files |
| get_splice_sites_info2 | Get all splice-sites and read-end positions of a BAM files |
| gt_vt_method | get the genotype and the variant type of the calls of a... |
| igv_batch_screenshots | Generate igv batch screenshots script |
| initiate_master_table | Initiate master table |
| is_indel_method | Add a column to state whether the variant is an indel or not |
| make_homopolymer_plot | Make plot to compare accuracy per homopolymer length |
| make_homopolymer_table_to_plot | Organize the data used to make plots about homopolymer... |
| method_homopolymer_indels | Get indels in homopolymers |
| precision_recall_curve_per_coverage | Precision-recall curves to compare methods, using different... |
| splice_junction_analysis_table | Generate data for splice-junction analysis using multiple... |
| standardize_genotype | Standardize genotypes |
