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

https://github.com/samtools/htslib
http://tclap.sourceforge.net
https://github.com/atks/Rmath
http://sourceforge.net/projects/pcre
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

Name		Name	Last commit message	Last commit date
lib		lib
test		test
.gitignore		.gitignore
.gitmodules		.gitmodules
.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

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