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

genome.sph.umich.edu/wiki/vt

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MIT license
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lib/include
lib/include
 
 
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_dbsnp_rsid.cpp
annotate_dbsnp_rsid.cpp
 
 
annotate_dbsnp_rsid.h
annotate_dbsnp_rsid.h
 
 
annotate_indel.cpp
annotate_indel.cpp
 
 
annotate_indel.h
annotate_indel.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
 
 
bam_ordered_reader.cpp
bam_ordered_reader.cpp
 
 
bam_ordered_reader.h
bam_ordered_reader.h
 
 
bam_variant_extractor.cpp
bam_variant_extractor.cpp
 
 
bam_variant_extractor.h
bam_variant_extractor.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.cpp
candidate_motif.cpp
 
 
candidate_motif.h
candidate_motif.h
 
 
cat.cpp
cat.cpp
 
 
cat.h
cat.h
 
 
chmm.cpp
chmm.cpp
 
 
chmm.h
chmm.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
 
 
config.cpp
config.cpp
 
 
config.h
config.h
 
 
consolidate_variants.cpp
consolidate_variants.cpp
 
 
consolidate_variants.h
consolidate_variants.h
 
 
construct_probes.cpp
construct_probes.cpp
 
 
construct_probes.h
construct_probes.h
 
 
context_filter.cpp
context_filter.cpp
 
 
context_filter.h
context_filter.h
 
 
decompose.cpp
decompose.cpp
 
 
decompose.h
decompose.h
 
 
decompose_blocksub.cpp
decompose_blocksub.cpp
 
 
decompose_blocksub.h
decompose_blocksub.h
 
 
discover.cpp
discover.cpp
 
 
discover.h
discover.h
 
 
discover2.cpp
discover2.cpp
 
 
discover2.h
discover2.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
 
 
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_buffer.cpp
genotyping_buffer.cpp
 
 
genotyping_buffer.h
genotyping_buffer.h
 
 
genotyping_record.h
genotyping_record.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
 
 
interval_tree.h
interval_tree.h
 
 
lfhmm.cpp
lfhmm.cpp
 
 
lfhmm.h
lfhmm.h
 
 
lhmm.cpp
lhmm.cpp
 
 
lhmm.h
lhmm.h
 
 
lhmm1.cpp
lhmm1.cpp
 
 
lhmm1.h
lhmm1.h
 
 
lhmm_genotyping_record.cpp
lhmm_genotyping_record.cpp
 
 
lhmm_genotyping_record.h
lhmm_genotyping_record.h
 
 
log_tool.cpp
log_tool.cpp
 
 
log_tool.h
log_tool.h
 
 
main.cpp
main.cpp
 
 
merge.cpp
merge.cpp
 
 
merge.h
merge.h
 
 
merge_candidate_variants.cpp
merge_candidate_variants.cpp
 
 
merge_candidate_variants.h
merge_candidate_variants.h
 
 
motif_suffix_tree.cpp
motif_suffix_tree.cpp
 
 
motif_suffix_tree.h
motif_suffix_tree.h
 
 
normalize.cpp
normalize.cpp
 
 
normalize.h
normalize.h
 
 

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

genome.sph.umich.edu/wiki/Vt

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