目录
- libadded htslib as a submodule5年前
- testupdated test outputs for decompose_blocksub6年前
- .gitignoreAdd libsvm.a to .gitignore9年前
- .gitmodulesadded htslib as a submodule5年前
- .travis.ymlAdding tests directory.11年前
- LICENSEmisc cleaning up of code.11年前
- MakefileAdd test for MNVs6年前
- Makefile.defaultadded Makefile.default for manual rollback8年前
- README.mdUpdate README.md10年前
- ahmm.cppmisc. changes to suppress warnings during compilation7年前
- ahmm.hremoved instantiations of LogTool and Estimator.9年前
- align.cppadded checks on definition of model components for alignments9年前
- align.hupdated htslib, RTL dynamic programming implementation of rfhmm9年前
- allele.cppadded support classes for genotyping9年前
- allele.hadded support classes for genotyping9年前
- annotate_1000g.cppupdated 1000g annotations and functions in hts_util.*11年前
- annotate_1000g.hcleaned up headers10年前
- annotate_dbsnp_rsid.cppmisc. changes11年前
- annotate_dbsnp_rsid.hcleaned up headers10年前
- annotate_indels.cpprenamed variables for perfect and total number of repeats from hmm10年前
- annotate_indels.hcleaned up headers10年前
- annotate_indels2.cppupdated with new version of annotate_indels2 for testing8年前
- annotate_indels2.hupdated with new version of annotate_indels2 for testing8年前
- annotate_indels3.cppported over annotate_indels3.*7年前
- annotate_regions.cppadded without regions options to annotate_regions8年前
- annotate_regions.hcleaned up headers10年前
- annotate_variants.cppupdated issues related to STR symbolic allele representation.10年前
- annotate_variants.hcleaned up headers10年前
- annotate_vntrs.cppmisc changes plus refactoring.9年前
- annotate_vntrs.hcleaned up headers10年前
- augmented_bam_record.cppmisc. changes10年前
- augmented_bam_record.hcleaned up headers10年前
- bam_ordered_reader.cpprestructured genotyping data structures10年前
- bam_ordered_reader.hcleaned up headers10年前
- bcf_genotyping_buffered_reader.cppLogTool and Estimator are now static classes.9年前
- bcf_genotyping_buffered_reader.hLogTool and Estimator are now static classes.9年前
- bcf_ordered_reader.cppedits to documentation on incorporating start coordinates overlap checking only8年前
- bcf_ordered_reader.hmisc. changes and order checking for bcf ordered reader8年前
- bcf_ordered_writer.cpp updated htslib and made some chabnges to avoid compiler warnings6年前
- bcf_ordered_writer.hcleaned up headers10年前
- bcf_single_genotyping_buffered_reader.cppadded class for sinbgle sample calling9年前
- bcf_single_genotyping_buffered_reader.hadded class for sinbgle sample calling9年前
- bcf_synced_reader.cppfixed memory leak in BCFOrderedReader and BCFSyncedReader10年前
- bcf_synced_reader.hensure that equivalent records will occur in the same order as input files for synced reader.8年前
- bed.cppmisc. changes8年前
- bed.hmisc changes plus refactoring.9年前
- candidate_motif_picker.cppreplaced back() and front() functions from string10年前
- candidate_motif_picker.hmisc. changes and added EX_MOTIF types to better represent alleles in exact alignment10年前
- candidate_region_extractor.cppmisc. changes9年前
- candidate_region_extractor.hadded functions for creating dummy records for testing purposes9年前
- cat.cppallow compresseion setting for cat, minor bug fix for compression settings.10年前
- cat.hcleaned up headers10年前
- chmm.cppmisc. changes to suppress warnings during compilation7年前
- chmm.hremoved instantiations of LogTool and Estimator.9年前
- circular_buffer.cppmisc changes. reduced memory usage for merge_candidate_variants10年前
- circular_buffer.hcleaned up headers10年前
- complex_genotyping_record.cppupdated htslib5年前
- complex_genotyping_record.hupdated htslib5年前
- compute_concordance.cppmiscellaneous updates11年前
- compute_concordance.hcleaned up headers10年前
- compute_features.cppupdated dependencies checking9年前
- compute_features.hcleaned up headers10年前
- compute_features2.cppremoved instantiations of LogTool and Estimator.9年前
- compute_features2.hcleaned up headers10年前
- compute_rl_dist.cppmoved get_canonical() to VNTR10年前
- compute_rl_dist.hmisc. changes10年前
- config.cppconfig updates for reference files10年前
- config.hcleaned up headers10年前
- consolidate.cppallows rfhmm to not match repeat units, ensures that motif candidates are present in indel fragment10年前
- consolidate.hcleaned up headers10年前
- consolidate_adjacent_vntrs.cppseparate logic for adjacent VNTR handling9年前
- consolidate_adjacent_vntrs.hseparate logic for adjacent VNTR handling9年前
- consolidate_multiallelics.cppadded REF/ALT field operations for filter, changed INFO field names for consolidate multiallelics9年前
- consolidate_multiallelics.hadded multiallelics consolidator classes10年前
- consolidate_vntrs.cppintegrated topmed3 changes from Hyun into main branch10年前
- consolidate_vntrs.hcleaned up headers10年前
- construct_probes.cpprestructured genotyping data structures10年前
- construct_probes.hcleaned up headers10年前
- decompose.cppfixed bug on updating integer type INFO fields of variable length G8年前
- decompose.hcleaned up headers10年前
- decompose2.cppadded decompose2.* and other changes10年前
- decompose2.hcleaned up headers10年前
- decompose_blocksub.cppAdd option to set MNV max distance6年前
- decompose_blocksub.hcleaned up headers10年前
- discover.cppminor changes in output messages and clearing up of comments8年前
- discover.hcleaned up headers10年前
- duplicate.cppadded duplicate.cpp and trio.cpp8年前
- duplicate.hupdated pedigree objects and added trio and duplicate objects8年前
- estimate.cppupdated dependencies checking9年前
- estimate.hmisc. changes10年前
- estimator.cppLogTool and Estimator are now static classes.9年前
- estimator.hLogTool and Estimator are now static classes.9年前
- extract_vntrs.cppmisc. changes10年前
- extract_vntrs.hmajor rewrites to programs involved in consolidatio of variants10年前
- filter.cppadded missing code for float varaible length support8年前
- filter.hadded support for variable length INFO fields in filter expressions8年前
- filter_overlap.cppremove_overlap => filter_overlap9年前
- filter_overlap.hremove_overlap => filter_overlap9年前
- flank_detector.cppminor changes9年前
- flank_detector.hminor changes9年前
- fuzzy_aligner.cppmisc. changes10年前
- fuzzy_aligner.hmisc. changes10年前
- fuzzy_partition.cppadded checking for bcf_sync_hdr in various places.6年前
- fuzzy_partition.hcleaned up headers10年前
- gencode.cppmisc changes plus refactoring.9年前
- gencode.hcleaned up headers10年前
- genome_interval.cppupdated htalib8年前
- genome_interval.hmisc changes plus refactoring.9年前
- genotype.cppsimplified framework for genotyping9年前
- genotype.hclearer division on genotyping modes.9年前
- genotyping_record.cpphousekeeping of codes9年前
- genotyping_record.hupdated htslib5年前
- ghmm.cppremoved instantiations of LogTool and Estimator.9年前
- ghmm.hremoved instantiations of LogTool and Estimator.9年前
- hfilter.cppadded motifTree11年前
- hfilter.hcleaned up headers10年前
- hts_utils.cppupdated libraries5年前
- hts_utils.h updated htslib and made some chabnges to avoid compiler warnings6年前
- indel_annotator.cppupdated with new version of annotate_indels2 for testing8年前
- indel_annotator.hupdated with new version of annotate_indels2 for testing8年前
- indel_genotyping_record.cpphousekeeping8年前
- indel_genotyping_record.hhousekeeping8年前
- index.cppworking version of vntr annotator where most hits are good but some misses are present10年前
- index.hcleaned up headers10年前
- info2tab.cppadded a check to ensure that annotate_regions must use an index BED file8年前
- info2tab.hadded info2tab for extracting info fields for plotting in R or further data processing9年前
- interval.cppmisc changes plus refactoring.9年前
- interval.hedits to documentation on incorporating start coordinates overlap checking only8年前
- interval_tree.cppmisc changes plus refactoring.9年前
- interval_tree.hcleaned up headers10年前
- large_motif_tree.cppmisc. changes9年前
- large_motif_tree.hfixes for G,A,R printouts9年前
- lfhmm.cppmisc. changes to suppress warnings during compilation7年前
- lfhmm.hremoved instantiations of LogTool and Estimator.9年前
- lhmm.cppremoved instantiations of LogTool and Estimator.9年前
- lhmm.hremoved instantiations of LogTool and Estimator.9年前
- lhmm1.cppremoved instantiations of LogTool and Estimator.9年前
- lhmm1.hremoved instantiations of LogTool and Estimator.9年前
- liftover.cppadded pseudo code for liftover.8年前
- liftover.hliftover skeleton files for VCF to include updating of headers and VCF specific flags8年前
- log_tool.cppLogTool and Estimator are now static classes.9年前
- log_tool.hLogTool and Estimator are now static classes.9年前
- main.cppliftover skeleton files for VCF to include updating of headers and VCF specific flags8年前
- merge.cppremoved instantiations of LogTool and Estimator.9年前
- merge.hcleaned up headers10年前
- merge_candidate_variants.cppremoved instantiations of LogTool and Estimator.9年前
- merge_candidate_variants.hmoved merge_candidate_variants2 to merge_candidate_variants10年前
- merge_genotypes.cppadded checking for bcf_sync_hdr in various places.6年前
- merge_genotypes.hclearer division on genotyping modes.9年前
- milk_filter.cpp updated htslib and made some chabnges to avoid compiler warnings6年前
- milk_filter.hadded documentation and house keeping.9年前
- motif_map.cppmisc. changes10年前
- motif_map.hmisc. changes, returns an error when random access is required for a VCF file.11年前
- motif_tree.cppadditional fixes to annotating multiallelic indels10年前
- motif_tree.hcleaned up headers10年前
- multi_partition.cppupdates to partition and multi_partition programs - in reporting and extra statistics and consistency in description.11年前
- multi_partition.hcleaned up headers10年前
- multiallelics_consolidator.cppremove_overlap => filter_overlap9年前
- multiallelics_consolidator.hadded REF/ALT field operations for filter, changed INFO field names for consolidate multiallelics9年前
- needle.cppremoved instantiations of LogTool and Estimator.9年前
- needle.hremoved instantiations of LogTool and Estimator.9年前
- normalize.cppmisc. changes9年前
- normalize.hcleaned up headers10年前
- nuclear_pedigree.cpphousekeeping of codes9年前
- nuclear_pedigree.hhousekeeping of codes9年前
- ordered_bcf_overlap_matcher.cppadded checking for bcf_sync_hdr in various places.6年前
- ordered_bcf_overlap_matcher.hmisc. changes and added EX_MOTIF types to better represent alleles in exact alignment10年前
- ordered_region_overlap_matcher.cppadded a check to ensure that annotate_regions must use an index BED file8年前
- ordered_region_overlap_matcher.hmisc changes plus refactoring.9年前
- partition.cppmisc changes10年前
- partition.hcleaned up headers10年前
- paste.cppupdated alternative header reading mechanism to only work for VCF files11年前
- paste.hcleaned up headers10年前
- paste_and_compute_features_sequential.cppLogTool and Estimator are now static classes.9年前
- paste_and_compute_features_sequential.hcleaned up headers10年前
- paste_genotypes.cppLogTool and Estimator are now static classes.9年前
- paste_genotypes.hmilk filter updates by Hyun.10年前
- pedigree.cppincluded site statistics output for pseudo autosomal regions8年前
- pedigree.hincluded site statistics output for pseudo autosomal regions8年前
- peek.cppmisc. changes10年前
- peek.hcleaned up headers10年前
- pileup.cppmisc. changes10年前
- pileup.hcleaned up headers10年前
- pregex.cppmisc changes, updated modularity of VNTR classification.10年前
- pregex.htweaks to filter and regex handling to allow for continuous usage of Filter object9年前
- profile_afs.cppcleaned up headers10年前
- profile_afs.hcleaned up headers10年前
- profile_chm1.cpphousekeeping8年前
- profile_chm1.hcleaned up headers10年前
- profile_chrom.cppcleaned up headers10年前
- profile_chrom.hcleaned up headers10年前
- profile_fic_hwe.cppcleaned up headers10年前
- profile_fic_hwe.hcleaned up headers10年前
- profile_hwe.cppmisc changes11年前
- profile_hwe.hcleaned up headers10年前
- profile_indels.cppmisc. changes8年前
- profile_indels.hcleaned up headers10年前
- profile_len.cppcleaned up headers10年前
- profile_len.hcleaned up headers10年前
- profile_mendelian.cppadded checking for bcf_sync_hdr in various places.6年前
- profile_mendelian.hupdated pedigree objects and added trio and duplicate objects8年前
- profile_na12878.cppdiscover only reports variants where REF contains only ACGT.10年前
- profile_na12878.hcleaned up headers10年前
- profile_snps.cppmisc. changes8年前
- profile_snps.hcleaned up headers10年前
- profile_vntrs.cppmisc. changes8年前
- profile_vntrs.hcleaned up headers10年前
- program.cppadded flag support9年前
- program.hmisc. changes, added some functions hts_utils to translate codes into human readable form9年前
- read_filter.cppadded class for sinbgle sample calling9年前
- read_filter.hupdated htslib8年前
- reference_sequence.cppadded functions for creating dummy records for testing purposes9年前
- reference_sequence.hadded functions for creating dummy records for testing purposes9年前
- rfhmm.cppmisc. changes to suppress warnings during compilation7年前
- rfhmm.hupdated htslib, RTL dynamic programming implementation of rfhmm9年前
- rfhmm_x.cppmisc. changes to suppress warnings during compilation7年前
- rfhmm_x.hadded rfhmm_x.*9年前
- rminfo.cppmisc. changes, added some functions hts_utils to translate codes into human readable form9年前
- rminfo.hcleaned up headers10年前
- seq.cppcleaned up headers10年前
- seq.hcleaned up headers10年前
- set_ref.cppmiusc. changes, added str genotyping modules9年前
- set_ref.hcleaned up headers10年前
- snp_genotyping_record.cpphousekeeping8年前
- snp_genotyping_record.hhousekeeping8年前
- sort.cppmisc changes10年前
- sort.hcleaned up headers10年前
- str_annotator.cppadded str annotator for classic representation5年前
- str_annotator.hadded str annotator for classic representation5年前
- subset.cppminor changes to exit the program when number of subset samples is 08年前
- subset.hcleaned up headers10年前
- sv_tree.cppfixed a bug in sv_tree in the usage of khash - char* key's memory allocation must always be managed by the user!!!!!11年前
- sv_tree.hcleaned up headers10年前
- svm_predict.cppmisc. changes and order checking for bcf ordered reader8年前
- svm_predict.hcleaned up headers10年前
- svm_train.cppnormalize into #uniq+1 buckets to avoid qnorm(1)9年前
- svm_train.hupdated htslib, updated inverse quantile normalization in svm_train9年前
- tbx_ordered_reader.cppadded a check to ensure that annotate_regions must use an index BED file8年前
- tbx_ordered_reader.hadded a check to ensure that annotate_regions must use an index BED file8年前
- test.cppminor changes9年前
- test.hcleaned up headers10年前
- trio.cppadded duplicate.cpp and trio.cpp8年前
- trio.hupdated pedigree objects and added trio and duplicate objects8年前
- union_variants.cpprenamed cross_compare.* and updated it11年前
- union_variants.hcleaned up headers10年前
- uniq.cppuniq now aggregates OLD_VARIANT tags.11年前
- uniq.hcleaned up headers10年前
- utils.cppupdated pedigree objects and added trio and duplicate objects8年前
- utils.hupdated pedigree objects and added trio and duplicate objects8年前
- validate.cppupdated validate to allow for case insensitive matching of reference11年前
- validate.hcleaned up headers10年前
- variant.cppupdated htslib and misc. changes9年前
- variant.hintegrated topmed3 changes from Hyun into main branch10年前
- variant_filter.cppmisc. changes10年前
- variant_filter.hcleaned up headers10年前
- variant_manip.cppupdated faidx_fetch_uc_seq7年前
- variant_manip.hmisc. changes, normalize to add extra level of strictness to not fail when encountering masked sequences.10年前
- version.hmisc. changes to suppress warnings during compilation7年前
- view.cppfixed bugs in profile_mendelian8年前
- view.hcleaned up headers10年前
- vntr.cppfixed silent bugs in indel annotation. + misc. changes9年前
- vntr.hrenamed variables for perfect and total number of repeats from hmm10年前
- vntr_annotator.cppfixed silent bugs in indel annotation. + misc. changes9年前
- vntr_annotator.hadded montgomery et al. classification of indels9年前
- vntr_consolidator.cppadded remaining setters and getters for INFO via a C++ interface.9年前
- vntr_consolidator.hupdated structure of vntr_consolidator for better statistic accounting and logic separation10年前
- vntr_extractor.cppmisc. changes9年前
- vntr_extractor.hmisc. changes9年前
- vntr_genotyping_record.cpphousekeeping8年前
- vntr_genotyping_record.hhousekeeping8年前
- vntr_tree.cppmisc. changes. updates basis from motif if not available in the info fields10年前
- vntr_tree.hcleaned up headers10年前
- vntrize.cppmisc. changes9年前
- vntrize.hcleaned up headers10年前
- wdp_ahmm.cppmisc. changes8年前
- wdp_ahmm.hmisc. changes8年前
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vt
A tool set for short variant discovery in genetic sequence data.
Visit http://genome.sph.umich.edu/wiki/vt for instructions.
vt uses htslib1, tclap2, Rmath3, pcre24 and libsvm5.
How to cite
vt normalize :
Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. Unified Representation of Genetic Variants. Bioinformatics (2015) 31(13): 2202-2204
Reference