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
Latest commit History 1,029 Commits
lib		lib
test		test
.gitignore		.gitignore
.travis.yml		.travis.yml
LICENSE		LICENSE
Makefile		Makefile
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_regions.cpp		annotate_regions.cpp
annotate_regions.h		annotate_regions.h
annotate_variants.cpp		annotate_variants.cpp
annotate_variants.h		annotate_variants.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_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
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
config.cpp		config.cpp
config.h		config.h
consolidate.cpp		consolidate.cpp
consolidate.h		consolidate.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
estimate.cpp		estimate.cpp
estimate.h		estimate.h
estimator.cpp		estimator.cpp
estimator.h		estimator.h
filter.cpp		filter.cpp
filter.h		filter.h
flank_detector.cpp		flank_detector.cpp
flank_detector.h		flank_detector.h
fuzzy_aligner.cpp		fuzzy_aligner.cpp
fuzzy_aligner.h		fuzzy_aligner.h
fuzzy_partition.cpp		fuzzy_partition.cpp
fuzzy_partition.h		fuzzy_partition.h
gencode.cpp		gencode.cpp
gencode.h		gencode.h
genome_interval.cpp		genome_interval.cpp
genome_interval.h		genome_interval.h
genotype.cpp		genotype.cpp
genotype.h		genotype.h
genotype2.cpp		genotype2.cpp
genotype2.h		genotype2.h
genotyping_record.cpp		genotyping_record.cpp
genotyping_record.h		genotyping_record.h
hfilter.cpp		hfilter.cpp
hfilter.h		hfilter.h
hts_utils.cpp		hts_utils.cpp
hts_utils.h		hts_utils.h
index.cpp		index.cpp
index.h		index.h
interval.cpp		interval.cpp
interval.h		interval.h
interval_tree.cpp		interval_tree.cpp

License

andyrimmer/vt

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