Skip to content
/ vt Public
forked from pkrusche/vt

A tool set for short variant discovery in genetic sequence data.

genome.sph.umich.edu/wiki/vt

License

MIT license
0 stars 37 forks Branches Tags Activity
Star
Notifications You must be signed in to change notification settings

MelanieBroutin/vt

BranchesTags
 
 

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

1,323 Commits
lib
lib
 
 
test
test
 
 
.gitignore
.gitignore
 
 
.travis.yml
.travis.yml
 
 
LICENSE
LICENSE
 
 
Makefile
Makefile
 
 
Makefile.default
Makefile.default
 
 
README.md
README.md
 
 
ahmm.cpp
ahmm.cpp
 
 
ahmm.h
ahmm.h
 
 
align.cpp
align.cpp
 
 
align.h
align.h
 
 
allele.cpp
allele.cpp
 
 
allele.h
allele.h
 
 
annotate_1000g.cpp
annotate_1000g.cpp
 
 
annotate_1000g.h
annotate_1000g.h
 
 
annotate_dbsnp_rsid.cpp
annotate_dbsnp_rsid.cpp
 
 
annotate_dbsnp_rsid.h
annotate_dbsnp_rsid.h
 
 
annotate_indels.cpp
annotate_indels.cpp
 
 
annotate_indels.h
annotate_indels.h
 
 
annotate_indels2.cpp
annotate_indels2.cpp
 
 
annotate_indels2.h
annotate_indels2.h
 
 
annotate_indels3.cpp
annotate_indels3.cpp
 
 
annotate_regions.cpp
annotate_regions.cpp
 
 
annotate_regions.h
annotate_regions.h
 
 
annotate_variants.cpp
annotate_variants.cpp
 
 
annotate_variants.h
annotate_variants.h
 
 
annotate_vntrs.cpp
annotate_vntrs.cpp
 
 
annotate_vntrs.h
annotate_vntrs.h
 
 
augmented_bam_record.cpp
augmented_bam_record.cpp
 
 
augmented_bam_record.h
augmented_bam_record.h
 
 
bam_ordered_reader.cpp
bam_ordered_reader.cpp
 
 
bam_ordered_reader.h
bam_ordered_reader.h
 
 
bcf_genotyping_buffered_reader.cpp
bcf_genotyping_buffered_reader.cpp
 
 
bcf_genotyping_buffered_reader.h
bcf_genotyping_buffered_reader.h
 
 
bcf_ordered_reader.cpp
bcf_ordered_reader.cpp
 
 
bcf_ordered_reader.h
bcf_ordered_reader.h
 
 
bcf_ordered_writer.cpp
bcf_ordered_writer.cpp
 
 
bcf_ordered_writer.h
bcf_ordered_writer.h
 
 
bcf_single_genotyping_buffered_reader.cpp
bcf_single_genotyping_buffered_reader.cpp
 
 
bcf_single_genotyping_buffered_reader.h
bcf_single_genotyping_buffered_reader.h
 
 
bcf_synced_reader.cpp
bcf_synced_reader.cpp
 
 
bcf_synced_reader.h
bcf_synced_reader.h
 
 
bed.cpp
bed.cpp
 
 
bed.h
bed.h
 
 
candidate_motif_picker.cpp
candidate_motif_picker.cpp
 
 
candidate_motif_picker.h
candidate_motif_picker.h
 
 
candidate_region_extractor.cpp
candidate_region_extractor.cpp
 
 
candidate_region_extractor.h
candidate_region_extractor.h
 
 
cat.cpp
cat.cpp
 
 
cat.h
cat.h
 
 
chmm.cpp
chmm.cpp
 
 
chmm.h
chmm.h
 
 
circular_buffer.cpp
circular_buffer.cpp
 
 
circular_buffer.h
circular_buffer.h
 
 
complex_genotyping_record.cpp
complex_genotyping_record.cpp
 
 
complex_genotyping_record.h
complex_genotyping_record.h
 
 
compute_concordance.cpp
compute_concordance.cpp
 
 
compute_concordance.h
compute_concordance.h
 
 
compute_features.cpp
compute_features.cpp
 
 
compute_features.h
compute_features.h
 
 
compute_features2.cpp
compute_features2.cpp
 
 
compute_features2.h
compute_features2.h
 
 
compute_rl_dist.cpp
compute_rl_dist.cpp
 
 
compute_rl_dist.h
compute_rl_dist.h
 
 
config.cpp
config.cpp
 
 
config.h
config.h
 
 
consolidate.cpp
consolidate.cpp
 
 
consolidate.h
consolidate.h
 
 
consolidate_adjacent_vntrs.cpp
consolidate_adjacent_vntrs.cpp
 
 
consolidate_adjacent_vntrs.h
consolidate_adjacent_vntrs.h
 
 
consolidate_multiallelics.cpp
consolidate_multiallelics.cpp
 
 
consolidate_multiallelics.h
consolidate_multiallelics.h
 
 
consolidate_vntrs.cpp
consolidate_vntrs.cpp
 
 
consolidate_vntrs.h
consolidate_vntrs.h
 
 
construct_probes.cpp
construct_probes.cpp
 
 
construct_probes.h
construct_probes.h
 
 
decompose.cpp
decompose.cpp
 
 
decompose.h
decompose.h
 
 
decompose2.cpp
decompose2.cpp
 
 
decompose2.h
decompose2.h
 
 
decompose_blocksub.cpp
decompose_blocksub.cpp
 
 
decompose_blocksub.h
decompose_blocksub.h
 
 
discover.cpp
discover.cpp
 
 
discover.h
discover.h
 
 
duplicate.cpp
duplicate.cpp
 
 
duplicate.h
duplicate.h
 
 
estimate.cpp
estimate.cpp
 
 
estimate.h
estimate.h
 
 
estimator.cpp
estimator.cpp
 
 
estimator.h
estimator.h
 
 
extract_vntrs.cpp
extract_vntrs.cpp
 
 
extract_vntrs.h
extract_vntrs.h
 
 
filter.cpp
filter.cpp
 
 
filter.h
filter.h
 
 
filter_overlap.cpp
filter_overlap.cpp
 
 
filter_overlap.h
filter_overlap.h
 
 
flank_detector.cpp
flank_detector.cpp
 
 
flank_detector.h
flank_detector.h
 
 
fuzzy_aligner.cpp
fuzzy_aligner.cpp
 
 

Repository files navigation

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

About

A tool set for short variant discovery in genetic sequence data.

genome.sph.umich.edu/wiki/vt

Resources

Readme

License

MIT license
Activity

Stars

0 stars

Watchers

0 watching

Forks

0 forks
Report repository

Releases

8 tags

Packages

No packages published

Languages

  • C 67.4%
  • C++ 30.0%
  • Perl 0.7%
  • Shell 0.7%
  • Makefile 0.5%
  • Roff 0.3%
  • Other 0.4%