A tool set for short variant discovery in genetic sequence data.
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Failed to load latest commit information.
lib updated htslib and modifications to bcf_ordered_writer Aug 1, 2018
test misc. changes May 18, 2016
.gitignore Add libsvm.a to .gitignore Oct 25, 2016
.travis.yml Adding tests directory. May 13, 2015
LICENSE misc cleaning up of code. Dec 31, 2014
Makefile for mac portability May 9, 2018
Makefile.default added Makefile.default for manual rollback Apr 5, 2018
README.md Update README.md Jan 16, 2016
ahmm.cpp misc. changes to suppress warnings during compilation Jul 13, 2018
ahmm.h removed instantiations of LogTool and Estimator. Oct 24, 2016
align.cpp added checks on definition of model components for alignments Dec 2, 2016
align.h updated htslib, RTL dynamic programming implementation of rfhmm Nov 2, 2016
allele.cpp added support classes for genotyping Dec 4, 2016
allele.h added support classes for genotyping Dec 4, 2016
annotate_1000g.cpp updated 1000g annotations and functions in hts_util.* Jun 8, 2015
annotate_1000g.h cleaned up headers Feb 15, 2016
annotate_dbsnp_rsid.cpp misc. changes Dec 29, 2014
annotate_dbsnp_rsid.h cleaned up headers Feb 15, 2016
annotate_indels.cpp renamed variables for perfect and total number of repeats from hmm Mar 23, 2016
annotate_indels.h cleaned up headers Feb 15, 2016
annotate_indels2.cpp updated with new version of annotate_indels2 for testing Nov 16, 2017
annotate_indels2.h updated with new version of annotate_indels2 for testing Nov 16, 2017
annotate_regions.cpp added without regions options to annotate_regions Nov 22, 2017
annotate_regions.h cleaned up headers Feb 15, 2016
annotate_variants.cpp updated issues related to STR symbolic allele representation. Feb 8, 2016
annotate_variants.h cleaned up headers Feb 15, 2016
annotate_vntrs.cpp misc changes plus refactoring. Sep 8, 2016
annotate_vntrs.h cleaned up headers Feb 15, 2016
augmented_bam_record.cpp misc. changes Sep 24, 2015
augmented_bam_record.h cleaned up headers Feb 15, 2016
bam_ordered_reader.cpp restructured genotyping data structures Aug 26, 2015
bam_ordered_reader.h cleaned up headers Feb 15, 2016
bcf_genotyping_buffered_reader.cpp LogTool and Estimator are now static classes. Oct 24, 2016
bcf_genotyping_buffered_reader.h LogTool and Estimator are now static classes. Oct 24, 2016
bcf_ordered_reader.cpp edits to documentation on incorporating start coordinates overlap che… Apr 6, 2018
bcf_ordered_reader.h misc. changes and order checking for bcf ordered reader Nov 19, 2017
bcf_ordered_writer.cpp updated htslib and modifications to bcf_ordered_writer Aug 1, 2018
bcf_ordered_writer.h cleaned up headers Feb 15, 2016
bcf_single_genotyping_buffered_reader.cpp added class for sinbgle sample calling Aug 1, 2016
bcf_single_genotyping_buffered_reader.h added class for sinbgle sample calling Aug 1, 2016
bcf_synced_reader.cpp fixed memory leak in BCFOrderedReader and BCFSyncedReader Dec 17, 2015
bcf_synced_reader.h ensure that equivalent records will occur in the same order as input … Nov 7, 2017
bed.cpp misc. changes Nov 7, 2017
bed.h misc changes plus refactoring. Sep 8, 2016
candidate_motif_picker.cpp replaced back() and front() functions from string Apr 20, 2016
candidate_motif_picker.h misc. changes and added EX_MOTIF types to better represent alleles in… Feb 25, 2016
candidate_region_extractor.cpp misc. changes Aug 21, 2016
candidate_region_extractor.h added functions for creating dummy records for testing purposes Aug 14, 2016
cat.cpp allow compresseion setting for cat, minor bug fix for compression set… Jan 8, 2016
cat.h cleaned up headers Feb 15, 2016
chmm.cpp misc. changes to suppress warnings during compilation Jul 13, 2018
chmm.h removed instantiations of LogTool and Estimator. Oct 24, 2016
circular_buffer.cpp misc changes. reduced memory usage for merge_candidate_variants Aug 22, 2015
circular_buffer.h cleaned up headers Feb 15, 2016
complex_genotyping_record.cpp LogTool and Estimator are now static classes. Oct 24, 2016
complex_genotyping_record.h LogTool and Estimator are now static classes. Oct 24, 2016
compute_concordance.cpp miscellaneous updates Jun 4, 2015
compute_concordance.h cleaned up headers Feb 15, 2016
compute_features.cpp updated dependencies checking Feb 4, 2017
compute_features.h cleaned up headers Feb 15, 2016
compute_features2.cpp removed instantiations of LogTool and Estimator. Oct 24, 2016
compute_features2.h cleaned up headers Feb 15, 2016
compute_rl_dist.cpp moved get_canonical() to VNTR Feb 19, 2016
compute_rl_dist.h misc. changes Feb 18, 2016
config.cpp config updates for reference files Oct 5, 2015
config.h cleaned up headers Feb 15, 2016
consolidate.cpp allows rfhmm to not match repeat units, ensures that motif candidates… Oct 6, 2015
consolidate.h cleaned up headers Feb 15, 2016
consolidate_adjacent_vntrs.cpp separate logic for adjacent VNTR handling Dec 6, 2016
consolidate_adjacent_vntrs.h separate logic for adjacent VNTR handling Dec 6, 2016
consolidate_multiallelics.cpp added REF/ALT field operations for filter, changed INFO field names f… Dec 27, 2016
consolidate_multiallelics.h added multiallelics consolidator classes Mar 9, 2016
consolidate_vntrs.cpp integrated topmed3 changes from Hyun into main branch May 16, 2016
consolidate_vntrs.h cleaned up headers Feb 15, 2016
construct_probes.cpp restructured genotyping data structures Aug 26, 2015
construct_probes.h cleaned up headers Feb 15, 2016
decompose.cpp fixed bug on updating integer type INFO fields of variable length G May 4, 2018
decompose.h cleaned up headers Feb 15, 2016
decompose2.cpp added decompose2.* and other changes Jun 15, 2015
decompose2.h cleaned up headers Feb 15, 2016
decompose_blocksub.cpp fixed decompose_blocksub for entries that have missing alleles in ALT… Jan 22, 2017
decompose_blocksub.h cleaned up headers Feb 15, 2016
discover.cpp minor changes in output messages and clearing up of comments Nov 16, 2017
discover.h cleaned up headers Feb 15, 2016
duplicate.cpp added duplicate.cpp and trio.cpp Nov 8, 2017
duplicate.h updated pedigree objects and added trio and duplicate objects Nov 8, 2017
estimate.cpp updated dependencies checking Feb 4, 2017
estimate.h misc. changes Feb 24, 2016
estimator.cpp LogTool and Estimator are now static classes. Oct 24, 2016
estimator.h LogTool and Estimator are now static classes. Oct 24, 2016
extract_vntrs.cpp misc. changes Mar 24, 2016
extract_vntrs.h major rewrites to programs involved in consolidatio of variants Mar 4, 2016
filter.cpp added missing code for float varaible length support Mar 5, 2018
filter.h added support for variable length INFO fields in filter expressions Mar 5, 2018
filter_overlap.cpp remove_overlap => filter_overlap Jan 12, 2017
filter_overlap.h remove_overlap => filter_overlap Jan 12, 2017
flank_detector.cpp minor changes Sep 1, 2016
flank_detector.h minor changes Sep 1, 2016
fuzzy_aligner.cpp misc. changes Feb 15, 2016
fuzzy_aligner.h misc. changes Feb 15, 2016
fuzzy_partition.cpp misc. changes Feb 29, 2016
fuzzy_partition.h cleaned up headers Feb 15, 2016
gencode.cpp misc changes plus refactoring. Sep 8, 2016
gencode.h cleaned up headers Feb 15, 2016
genome_interval.cpp updated htalib May 1, 2018
genome_interval.h misc changes plus refactoring. Sep 8, 2016
genotype.cpp simplified framework for genotyping Oct 19, 2016
genotype.h clearer division on genotyping modes. Aug 2, 2016
genotyping_record.cpp housekeeping of codes Aug 9, 2016
genotyping_record.h LogTool and Estimator are now static classes. Oct 24, 2016
ghmm.cpp removed instantiations of LogTool and Estimator. Oct 24, 2016
ghmm.h removed instantiations of LogTool and Estimator. Oct 24, 2016
hfilter.cpp added motifTree Apr 7, 2015
hfilter.h cleaned up headers Feb 15, 2016
hts_utils.cpp misc. changes to suppress warnings during compilation Jul 13, 2018
hts_utils.h removed faidx_t definition in hts_utils.h Jul 15, 2018
indel_annotator.cpp updated with new version of annotate_indels2 for testing Nov 16, 2017
indel_annotator.h updated with new version of annotate_indels2 for testing Nov 16, 2017
indel_genotyping_record.cpp housekeeping Mar 4, 2018
indel_genotyping_record.h housekeeping Mar 4, 2018
index.cpp working version of vntr annotator where most hits are good but some m… Sep 22, 2015
index.h cleaned up headers Feb 15, 2016
info2tab.cpp added a check to ensure that annotate_regions must use an index BED file Nov 13, 2017
info2tab.h added info2tab for extracting info fields for plotting in R or furthe… Aug 17, 2016
interval.cpp misc changes plus refactoring. Sep 8, 2016
interval.h edits to documentation on incorporating start coordinates overlap che… Apr 6, 2018
interval_tree.cpp misc changes plus refactoring. Sep 8, 2016
interval_tree.h cleaned up headers Feb 15, 2016
large_motif_tree.cpp misc. changes Aug 26, 2016
large_motif_tree.h fixes for G,A,R printouts Aug 27, 2016
lfhmm.cpp misc. changes to suppress warnings during compilation Jul 13, 2018
lfhmm.h removed instantiations of LogTool and Estimator. Oct 24, 2016
lhmm.cpp removed instantiations of LogTool and Estimator. Oct 24, 2016
lhmm.h removed instantiations of LogTool and Estimator. Oct 24, 2016
lhmm1.cpp removed instantiations of LogTool and Estimator. Oct 24, 2016
lhmm1.h removed instantiations of LogTool and Estimator. Oct 24, 2016
liftover.cpp added pseudo code for liftover. Apr 3, 2018
liftover.h liftover skeleton files for VCF to include updating of headers and VC… Apr 3, 2018
log_tool.cpp LogTool and Estimator are now static classes. Oct 24, 2016
log_tool.h LogTool and Estimator are now static classes. Oct 24, 2016
main.cpp liftover skeleton files for VCF to include updating of headers and VC… Apr 3, 2018
merge.cpp removed instantiations of LogTool and Estimator. Oct 24, 2016
merge.h cleaned up headers Feb 15, 2016
merge_candidate_variants.cpp removed instantiations of LogTool and Estimator. Oct 24, 2016
merge_candidate_variants.h moved merge_candidate_variants2 to merge_candidate_variants Mar 22, 2016
merge_genotypes.cpp misc. changes and order checking for bcf ordered reader Nov 19, 2017
merge_genotypes.h clearer division on genotyping modes. Aug 2, 2016
milk_filter.cpp removed instantiations of LogTool and Estimator. Oct 24, 2016
milk_filter.h added documentation and house keeping. Aug 10, 2016
motif_map.cpp misc. changes Dec 3, 2015
motif_map.h misc. changes, returns an error when random access is required for a … Apr 23, 2015
motif_tree.cpp additional fixes to annotating multiallelic indels Dec 1, 2015
motif_tree.h cleaned up headers Feb 15, 2016
multi_partition.cpp updates to partition and multi_partition programs - in reporting and … May 14, 2015
multi_partition.h cleaned up headers Feb 15, 2016
multiallelics_consolidator.cpp remove_overlap => filter_overlap Jan 12, 2017
multiallelics_consolidator.h added REF/ALT field operations for filter, changed INFO field names f… Dec 27, 2016
needle.cpp removed instantiations of LogTool and Estimator. Oct 24, 2016
needle.h removed instantiations of LogTool and Estimator. Oct 24, 2016
normalize.cpp misc. changes Aug 7, 2016
normalize.h cleaned up headers Feb 15, 2016
nuclear_pedigree.cpp housekeeping of codes Aug 9, 2016
nuclear_pedigree.h housekeeping of codes Aug 9, 2016
ordered_bcf_overlap_matcher.cpp misc. changes and added EX_MOTIF types to better represent alleles in… Feb 25, 2016
ordered_bcf_overlap_matcher.h misc. changes and added EX_MOTIF types to better represent alleles in… Feb 25, 2016
ordered_region_overlap_matcher.cpp added a check to ensure that annotate_regions must use an index BED file Nov 13, 2017
ordered_region_overlap_matcher.h misc changes plus refactoring. Sep 8, 2016
partition.cpp misc changes Dec 13, 2015
partition.h cleaned up headers Feb 15, 2016
paste.cpp updated alternative header reading mechanism to only work for VCF files Jun 8, 2015
paste.h cleaned up headers Feb 15, 2016
paste_and_compute_features_sequential.cpp LogTool and Estimator are now static classes. Oct 24, 2016
paste_and_compute_features_sequential.h cleaned up headers Feb 15, 2016
paste_genotypes.cpp LogTool and Estimator are now static classes. Oct 24, 2016
paste_genotypes.h milk filter updates by Hyun. Mar 21, 2016
pedigree.cpp included site statistics output for pseudo autosomal regions Nov 19, 2017
pedigree.h included site statistics output for pseudo autosomal regions Nov 19, 2017
peek.cpp misc. changes Mar 24, 2016
peek.h cleaned up headers Feb 15, 2016
pileup.cpp misc. changes Sep 25, 2015
pileup.h cleaned up headers Feb 15, 2016
pregex.cpp misc changes, updated modularity of VNTR classification. Jun 25, 2015
pregex.h tweaks to filter and regex handling to allow for continuous usage of … Dec 9, 2016
profile_afs.cpp cleaned up headers Feb 15, 2016
profile_afs.h cleaned up headers Feb 15, 2016
profile_chm1.cpp housekeeping Mar 4, 2018
profile_chm1.h cleaned up headers Feb 15, 2016
profile_chrom.cpp cleaned up headers Feb 15, 2016
profile_chrom.h cleaned up headers Feb 15, 2016
profile_fic_hwe.cpp cleaned up headers Feb 15, 2016
profile_fic_hwe.h cleaned up headers Feb 15, 2016
profile_hwe.cpp misc changes Mar 10, 2015
profile_hwe.h cleaned up headers Feb 15, 2016
profile_indels.cpp misc. changes Nov 7, 2017
profile_indels.h cleaned up headers Feb 15, 2016
profile_len.cpp cleaned up headers Feb 15, 2016
profile_len.h cleaned up headers Feb 15, 2016
profile_mendelian.cpp fixed bugs in profile_mendelian Nov 23, 2017
profile_mendelian.h updated pedigree objects and added trio and duplicate objects Nov 8, 2017
profile_na12878.cpp discover only reports variants where REF contains only ACGT. Apr 6, 2016
profile_na12878.h cleaned up headers Feb 15, 2016
profile_snps.cpp misc. changes Nov 7, 2017
profile_snps.h cleaned up headers Feb 15, 2016
profile_vntrs.cpp misc. changes Nov 7, 2017
profile_vntrs.h cleaned up headers Feb 15, 2016
program.cpp added flag support Aug 18, 2016
program.h misc. changes, added some functions hts_utils to translate codes into… Aug 17, 2016
read_filter.cpp added class for sinbgle sample calling Aug 1, 2016
read_filter.h updated htslib Apr 3, 2018
reference_sequence.cpp added functions for creating dummy records for testing purposes Aug 14, 2016
reference_sequence.h added functions for creating dummy records for testing purposes Aug 14, 2016
rfhmm.cpp misc. changes to suppress warnings during compilation Jul 13, 2018
rfhmm.h updated htslib, RTL dynamic programming implementation of rfhmm Nov 2, 2016
rfhmm_x.cpp misc. changes to suppress warnings during compilation Jul 13, 2018
rfhmm_x.h added rfhmm_x.* Nov 2, 2016
rminfo.cpp misc. changes, added some functions hts_utils to translate codes into… Aug 17, 2016
rminfo.h cleaned up headers Feb 15, 2016
seq.cpp cleaned up headers Feb 15, 2016
seq.h cleaned up headers Feb 15, 2016
set_ref.cpp miusc. changes, added str genotyping modules Jan 1, 2017
set_ref.h cleaned up headers Feb 15, 2016
snp_genotyping_record.cpp housekeeping Mar 4, 2018
snp_genotyping_record.h housekeeping Mar 4, 2018
sort.cpp misc changes Jun 28, 2015
sort.h cleaned up headers Feb 15, 2016
subset.cpp minor changes to exit the program when number of subset samples is 0 Nov 23, 2017
subset.h cleaned up headers Feb 15, 2016
sv_tree.cpp fixed a bug in sv_tree in the usage of khash - char* key's memory all… Feb 21, 2015
sv_tree.h cleaned up headers Feb 15, 2016
svm_predict.cpp misc. changes and order checking for bcf ordered reader Nov 19, 2017
svm_predict.h cleaned up headers Feb 15, 2016
svm_train.cpp normalize into #uniq+1 buckets to avoid qnorm(1) Jan 8, 2017
svm_train.h updated htslib, updated inverse quantile normalization in svm_train Jan 6, 2017
tbx_ordered_reader.cpp added a check to ensure that annotate_regions must use an index BED file Nov 13, 2017
tbx_ordered_reader.h added a check to ensure that annotate_regions must use an index BED file Nov 13, 2017
test.cpp minor changes Mar 22, 2017
test.h cleaned up headers Feb 15, 2016
trio.cpp added duplicate.cpp and trio.cpp Nov 8, 2017
trio.h updated pedigree objects and added trio and duplicate objects Nov 8, 2017
union_variants.cpp renamed cross_compare.* and updated it Dec 26, 2014
union_variants.h cleaned up headers Feb 15, 2016
uniq.cpp uniq now aggregates OLD_VARIANT tags. May 8, 2015
uniq.h cleaned up headers Feb 15, 2016
utils.cpp updated pedigree objects and added trio and duplicate objects Nov 8, 2017
utils.h updated pedigree objects and added trio and duplicate objects Nov 8, 2017
validate.cpp updated validate to allow for case insensitive matching of reference Feb 26, 2015
validate.h cleaned up headers Feb 15, 2016
variant.cpp updated htslib and misc. changes Aug 5, 2016
variant.h integrated topmed3 changes from Hyun into main branch May 16, 2016
variant_filter.cpp misc. changes Sep 24, 2015
variant_filter.h cleaned up headers Feb 15, 2016
variant_manip.cpp updated faidx_fetch_uc_seq Jul 13, 2018
variant_manip.h misc. changes, normalize to add extra level of strictness to not fail… Mar 19, 2016
version.h misc. changes to suppress warnings during compilation Jul 13, 2018
view.cpp fixed bugs in profile_mendelian Nov 23, 2017
view.h cleaned up headers Feb 15, 2016
vntr.cpp fixed silent bugs in indel annotation. + misc. changes Aug 31, 2016
vntr.h renamed variables for perfect and total number of repeats from hmm Mar 23, 2016
vntr_annotator.cpp fixed silent bugs in indel annotation. + misc. changes Aug 31, 2016
vntr_annotator.h added montgomery et al. classification of indels Aug 19, 2016
vntr_consolidator.cpp added remaining setters and getters for INFO via a C++ interface. Aug 22, 2016
vntr_consolidator.h updated structure of vntr_consolidator for better statistic accountin… Apr 11, 2016
vntr_extractor.cpp misc. changes Aug 21, 2016
vntr_extractor.h misc. changes Aug 21, 2016
vntr_genotyping_record.cpp housekeeping Mar 4, 2018
vntr_genotyping_record.h housekeeping Mar 4, 2018
vntr_tree.cpp misc. changes. updates basis from motif if not available in the info … Mar 9, 2016
vntr_tree.h cleaned up headers Feb 15, 2016
vntrize.cpp misc. changes Aug 26, 2016
vntrize.h cleaned up headers Feb 15, 2016
wdp_ahmm.cpp misc. changes Nov 7, 2017
wdp_ahmm.h misc. changes Nov 7, 2017

README.md

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

  1. https://github.com/samtools/htslib
  2. http://tclap.sourceforge.net
  3. https://github.com/atks/Rmath
  4. http://sourceforge.net/projects/pcre
  5. Chih-Chung Chang and Chih-Jen Lin, LIBSVM : a library for support vector machines. ACM Transactions on Intelligent Systems and Technology, 2:27:1--27:27, 2011. https://github.com/cjlin1/libsvm