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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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shukwong/vt

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This branch is 597 commits ahead of, 266 commits behind pkrusche/vt:master.

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atksatks
added bcf_2g2c()
Feb 1, 2015
9aa6108 · Feb 1, 2015

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597 Commits
lib/include
lib/include
Dec 17, 2014
LICENSE
LICENSE
Dec 31, 2014
Makefile
Makefile
Jan 27, 2015
README.md
README.md
Nov 19, 2014
ahmm.cpp
ahmm.cpp
Oct 13, 2014
ahmm.h
ahmm.h
Oct 13, 2014
align.cpp
align.cpp
Oct 8, 2014
align.h
align.h
Oct 8, 2014
allele.cpp
allele.cpp
Jan 23, 2015
allele.h
allele.h
Jan 23, 2015
annotate_dbsnp_rsid.cpp
annotate_dbsnp_rsid.cpp
Dec 29, 2014
annotate_dbsnp_rsid.h
annotate_dbsnp_rsid.h
Jun 19, 2014
annotate_indel.cpp
annotate_indel.cpp
Dec 29, 2014
annotate_indel.h
annotate_indel.h
Nov 12, 2014
annotate_regions.cpp
annotate_regions.cpp
Jan 27, 2015
annotate_regions.h
annotate_regions.h
May 9, 2014
annotate_variants.cpp
annotate_variants.cpp
Sep 9, 2014
annotate_variants.h
annotate_variants.h
Sep 3, 2014
bam_ordered_reader.cpp
bam_ordered_reader.cpp
Jun 20, 2014
bam_ordered_reader.h
bam_ordered_reader.h
Dec 14, 2014
bam_variant_extractor.cpp
bam_variant_extractor.cpp
Oct 6, 2014
bam_variant_extractor.h
bam_variant_extractor.h
Oct 6, 2014
bcf_ordered_reader.cpp
bcf_ordered_reader.cpp
Dec 17, 2014
bcf_ordered_reader.h
bcf_ordered_reader.h
Dec 15, 2014
bcf_ordered_writer.cpp
bcf_ordered_writer.cpp
Jan 27, 2015
bcf_ordered_writer.h
bcf_ordered_writer.h
Jan 27, 2015
bcf_synced_reader.cpp
bcf_synced_reader.cpp
Dec 22, 2014
bcf_synced_reader.h
bcf_synced_reader.h
Dec 22, 2014
bed.cpp
bed.cpp
Dec 30, 2014
bed.h
bed.h
May 7, 2014
candidate_motif.cpp
candidate_motif.cpp
Dec 30, 2014
candidate_motif.h
candidate_motif.h
Oct 29, 2014
cat.cpp
cat.cpp
Dec 17, 2014
cat.h
cat.h
Dec 14, 2014
chmm.cpp
chmm.cpp
Jun 26, 2014
chmm.h
chmm.h
Jun 10, 2014
compute_concordance.cpp
compute_concordance.cpp
Jan 30, 2015
compute_concordance.h
compute_concordance.h
Dec 3, 2013
compute_features.cpp
compute_features.cpp
Nov 12, 2014
compute_features.h
compute_features.h
Apr 27, 2014
config.cpp
config.cpp
Sep 25, 2014
config.h
config.h
Jun 30, 2014
consolidate_variants.cpp
consolidate_variants.cpp
Jun 3, 2014
consolidate_variants.h
consolidate_variants.h
May 30, 2014
construct_probes.cpp
construct_probes.cpp
Jan 15, 2014
construct_probes.h
construct_probes.h
Nov 25, 2013
context_filter.cpp
context_filter.cpp
Dec 31, 2014
context_filter.h
context_filter.h
Sep 11, 2014
decompose.cpp
decompose.cpp
Jan 29, 2015
decompose.h
decompose.h
Jan 25, 2014
decompose_blocksub.cpp
decompose_blocksub.cpp
Dec 31, 2014
decompose_blocksub.h
decompose_blocksub.h
Sep 22, 2014
discover.cpp
discover.cpp
Jun 23, 2014
discover.h
discover.h
Dec 3, 2013
discover2.cpp
discover2.cpp
Oct 6, 2014
discover2.h
discover2.h
Sep 22, 2014
estimate.cpp
estimate.cpp
Dec 24, 2014
estimate.h
estimate.h
Dec 12, 2014
estimator.cpp
estimator.cpp
Jun 16, 2014
estimator.h
estimator.h
Jun 16, 2014
filter.cpp
filter.cpp
Jan 29, 2015
filter.h
filter.h
Jan 21, 2015
gencode.cpp
gencode.cpp
Jun 23, 2014
gencode.h
gencode.h
Apr 30, 2014
genome_interval.cpp
genome_interval.cpp
Dec 5, 2014
genome_interval.h
genome_interval.h
May 5, 2014
genotype.cpp
genotype.cpp
Aug 8, 2014
genotype.h
genotype.h
Jan 15, 2014
genotype2.cpp
genotype2.cpp
Sep 19, 2014
genotype2.h
genotype2.h
Jun 12, 2014
genotyping_buffer.cpp
genotyping_buffer.cpp
Jan 15, 2014
genotyping_buffer.h
genotyping_buffer.h
Mar 18, 2014
genotyping_record.h
genotyping_record.h
Mar 18, 2014
hts_utils.cpp
hts_utils.cpp
Feb 1, 2015
hts_utils.h
hts_utils.h
Feb 1, 2015
index.cpp
index.cpp
Dec 13, 2014
index.h
index.h
Dec 4, 2014
interval.cpp
interval.cpp
Dec 30, 2014
interval.h
interval.h
Dec 30, 2014
interval_tree.cpp
interval_tree.cpp
Apr 30, 2014
interval_tree.h
interval_tree.h
Dec 30, 2014
lfhmm.cpp
lfhmm.cpp
Dec 31, 2014
lfhmm.h
lfhmm.h
Dec 14, 2014
lhmm.cpp
lhmm.cpp
Feb 20, 2014
lhmm.h
lhmm.h
Feb 20, 2014
lhmm1.cpp
lhmm1.cpp
Aug 8, 2014
lhmm1.h
lhmm1.h
Dec 14, 2014
lhmm_genotyping_record.cpp
lhmm_genotyping_record.cpp
Mar 18, 2014
lhmm_genotyping_record.h
lhmm_genotyping_record.h
Mar 12, 2014
log_tool.cpp
log_tool.cpp
Apr 21, 2014
log_tool.h
log_tool.h
Dec 14, 2014
main.cpp
main.cpp
Jan 31, 2015
merge.cpp
merge.cpp
Jun 20, 2014
merge.h
merge.h
Dec 14, 2014
merge_candidate_variants.cpp
merge_candidate_variants.cpp
Jan 23, 2015
merge_candidate_variants.h
merge_candidate_variants.h
Dec 14, 2014
motif_suffix_tree.cpp
motif_suffix_tree.cpp
Nov 12, 2014
motif_suffix_tree.h
motif_suffix_tree.h
Nov 12, 2014
normalize.cpp
normalize.cpp
Jan 27, 2015
normalize.h
normalize.h
Mar 7, 2014
ordered_bcf_overlap_matcher.cpp
ordered_bcf_overlap_matcher.cpp
Jan 29, 2015
ordered_bcf_overlap_matcher.h
ordered_bcf_overlap_matcher.h
Jan 27, 2015
ordered_region_overlap_matcher.cpp
ordered_region_overlap_matcher.cpp
Sep 17, 2014
ordered_region_overlap_matcher.h
ordered_region_overlap_matcher.h
May 7, 2014
partition.cpp
partition.cpp
Dec 14, 2014
partition.h
partition.h
Dec 14, 2014
paste.cpp
paste.cpp
Dec 24, 2014
paste.h
paste.h
Dec 15, 2014
pedigree.cpp
pedigree.cpp
May 1, 2014
pedigree.h
pedigree.h
May 1, 2014
peek.cpp
peek.cpp
Jan 29, 2015
peek.h
peek.h
Dec 14, 2014
profile_afs.cpp
profile_afs.cpp
Aug 13, 2014
profile_afs.h
profile_afs.h
Apr 30, 2014
profile_chm1.cpp
profile_chm1.cpp
Dec 29, 2014
profile_chm1.h
profile_chm1.h
Dec 29, 2014
profile_chrom.cpp
profile_chrom.cpp
Aug 11, 2014
profile_chrom.h
profile_chrom.h
May 7, 2014
profile_fic_hwe.cpp
profile_fic_hwe.cpp
Dec 11, 2014
profile_fic_hwe.h
profile_fic_hwe.h
Sep 10, 2014
profile_hwe.cpp
profile_hwe.cpp
Dec 31, 2014
profile_hwe.h
profile_hwe.h
Apr 30, 2014
profile_indels.cpp
profile_indels.cpp
Dec 11, 2014
profile_indels.h
profile_indels.h
Sep 17, 2014
profile_len.cpp
profile_len.cpp
Dec 31, 2014
profile_len.h
profile_len.h
May 1, 2014
profile_mendelian.cpp
profile_mendelian.cpp
Dec 31, 2014
profile_mendelian.h
profile_mendelian.h
May 1, 2014
profile_na12878.cpp
profile_na12878.cpp
Dec 11, 2014
profile_na12878.h
profile_na12878.h
Sep 17, 2014
profile_snps.cpp
profile_snps.cpp
Dec 11, 2014
profile_snps.h
profile_snps.h
Sep 17, 2014
program.cpp
program.cpp
Sep 24, 2014
program.h
program.h
Sep 24, 2014
remove_overlap.cpp
remove_overlap.cpp
Dec 17, 2014
remove_overlap.h
remove_overlap.h
Jan 29, 2014
rfhmm.cpp
rfhmm.cpp
Oct 7, 2014
rfhmm.h
rfhmm.h
Oct 7, 2014
seq.cpp
seq.cpp
Jan 23, 2015
seq.h
seq.h
Jan 19, 2015
sort.cpp
sort.cpp
Dec 31, 2014
sort.h
sort.h
Dec 13, 2014
str.cpp
str.cpp
Nov 12, 2014
str.h
str.h
Nov 4, 2014
subset.cpp
subset.cpp
Dec 3, 2014
subset.h
subset.h
Apr 23, 2014
sv_tree.cpp
sv_tree.cpp
Nov 12, 2014
sv_tree.h
sv_tree.h
Aug 28, 2014
tbx_ordered_reader.cpp
tbx_ordered_reader.cpp
May 6, 2014
tbx_ordered_reader.h
tbx_ordered_reader.h
May 5, 2014
test.cpp
test.cpp
Feb 1, 2015
test.h
test.h
May 9, 2014
union_variants.cpp
union_variants.cpp
Dec 26, 2014
union_variants.h
union_variants.h
Dec 14, 2014
uniq.cpp
uniq.cpp
Dec 22, 2014
uniq.h
uniq.h
Dec 22, 2014
utils.cpp
utils.cpp
Sep 5, 2014
utils.h
utils.h
Aug 15, 2014
validate.cpp
validate.cpp
Dec 14, 2014
validate.h
validate.h
Dec 14, 2014
variant.cpp
variant.cpp
Jan 23, 2015
variant.h
variant.h
Jan 23, 2015
variant_buffer.cpp
variant_buffer.cpp
Sep 25, 2014
variant_buffer.h
variant_buffer.h
Dec 14, 2014
variant_manip.cpp
variant_manip.cpp
Jan 25, 2015
variant_manip.h
variant_manip.h
Jan 23, 2015
view.cpp
view.cpp
Dec 17, 2014
view.h
view.h
Dec 14, 2014
vntrize.cpp
vntrize.cpp
Jan 29, 2015
vntrize.h
vntrize.h
Jan 27, 2015
xcmp.cpp
xcmp.cpp
Dec 28, 2014
xcmp.h
xcmp.h
Dec 26, 2014

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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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