vt

(β˜… 207)

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

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  • .gitignore
  • .gitmodules
  • .travis.yml
  • ahmm.cpp
  • ahmm.h
  • align.cpp
  • align.h
  • allele.cpp
  • allele.h
  • annotate_1000g.cpp
  • annotate_1000g.h
  • annotate_dbsnp_rsid.cpp
  • annotate_dbsnp_rsid.h
  • annotate_indels.cpp
  • annotate_indels.h
  • annotate_indels2.cpp
  • annotate_indels2.h
  • annotate_indels3.cpp
  • annotate_regions.cpp
  • annotate_regions.h
  • annotate_variants.cpp
  • annotate_variants.h
  • annotate_vntrs.cpp
  • annotate_vntrs.h
  • augmented_bam_record.cpp
  • augmented_bam_record.h
  • bam_ordered_reader.cpp
  • bam_ordered_reader.h
  • bcf_genotyping_buffered_reader.cpp
  • bcf_genotyping_buffered_reader.h
  • bcf_ordered_reader.cpp
  • bcf_ordered_reader.h
  • bcf_ordered_writer.cpp
  • bcf_ordered_writer.h
  • bcf_single_genotyping_buffered_reader.cpp
  • bcf_single_genotyping_buffered_reader.h
  • bcf_synced_reader.cpp
  • bcf_synced_reader.h
  • bed.cpp
  • bed.h
  • candidate_motif_picker.cpp
  • candidate_motif_picker.h
  • candidate_region_extractor.cpp
  • candidate_region_extractor.h
  • cat.cpp
  • cat.h
  • chmm.cpp
  • chmm.h
  • circular_buffer.cpp
  • circular_buffer.h
  • complex_genotyping_record.cpp
  • complex_genotyping_record.h
  • compute_concordance.cpp
  • compute_concordance.h
  • compute_features.cpp
  • compute_features.h
  • compute_features2.cpp
  • compute_features2.h
  • compute_rl_dist.cpp
  • compute_rl_dist.h
  • config.cpp
  • config.h
  • consolidate.cpp
  • consolidate.h
  • consolidate_adjacent_vntrs.cpp
  • consolidate_adjacent_vntrs.h
  • consolidate_multiallelics.cpp
  • consolidate_multiallelics.h
  • consolidate_vntrs.cpp
  • consolidate_vntrs.h
  • construct_probes.cpp
  • construct_probes.h
  • decompose.cpp
  • decompose.h
  • decompose2.cpp
  • decompose2.h
  • decompose_blocksub.cpp
  • decompose_blocksub.h
  • discover.cpp
  • discover.h
  • duplicate.cpp
  • duplicate.h
  • estimate.cpp
  • estimate.h
  • estimator.cpp
  • estimator.h
  • extract_vntrs.cpp
  • extract_vntrs.h
  • filter.cpp
  • filter.h
  • filter_overlap.cpp
  • filter_overlap.h
  • flank_detector.cpp
  • flank_detector.h
  • fuzzy_aligner.cpp
  • fuzzy_aligner.h
  • fuzzy_partition.cpp
  • fuzzy_partition.h
  • gencode.cpp
  • gencode.h
  • genome_interval.cpp
  • genome_interval.h
  • genotype.cpp
  • genotype.h
  • genotyping_record.cpp
  • genotyping_record.h
  • ghmm.cpp
  • ghmm.h
  • hfilter.cpp
  • hfilter.h
  • hts_utils.cpp
  • hts_utils.h
  • indel_annotator.cpp
  • indel_annotator.h
  • indel_genotyping_record.cpp
  • indel_genotyping_record.h
  • index.cpp
  • index.h
  • info2tab.cpp
  • info2tab.h
  • interval.cpp
  • interval.h
  • interval_tree.cpp
  • interval_tree.h
  • large_motif_tree.cpp
  • large_motif_tree.h
  • lfhmm.cpp
  • lfhmm.h
  • lhmm.cpp
  • lhmm.h
  • lhmm1.cpp
  • lhmm1.h
  • LICENSE
  • liftover.cpp
  • liftover.h
  • log_tool.cpp
  • log_tool.h
  • main.cpp
  • Makefile
  • Makefile.default
  • merge.cpp
  • merge.h
  • merge_candidate_variants.cpp
  • merge_candidate_variants.h
  • merge_genotypes.cpp
  • merge_genotypes.h
  • milk_filter.cpp
  • milk_filter.h
  • motif_map.cpp
  • motif_map.h
  • motif_tree.cpp
  • motif_tree.h
  • multi_partition.cpp
  • multi_partition.h
  • multiallelics_consolidator.cpp
  • multiallelics_consolidator.h
  • needle.cpp
  • needle.h
  • normalize.cpp
  • normalize.h
  • nuclear_pedigree.cpp
  • nuclear_pedigree.h
  • ordered_bcf_overlap_matcher.cpp
  • ordered_bcf_overlap_matcher.h
  • ordered_region_overlap_matcher.cpp
  • ordered_region_overlap_matcher.h
  • partition.cpp
  • partition.h
  • paste.cpp
  • paste.h
  • paste_and_compute_features_sequential.cpp
  • paste_and_compute_features_sequential.h
  • paste_genotypes.cpp
  • paste_genotypes.h
  • pedigree.cpp
  • pedigree.h
  • peek.cpp
  • peek.h
  • pileup.cpp
  • pileup.h
  • pregex.cpp
  • pregex.h
  • profile_afs.cpp
  • profile_afs.h
  • profile_chm1.cpp
  • profile_chm1.h
  • profile_chrom.cpp
  • profile_chrom.h
  • profile_fic_hwe.cpp
  • profile_fic_hwe.h
  • profile_hwe.cpp
  • profile_hwe.h
  • profile_indels.cpp
  • profile_indels.h
  • profile_len.cpp
  • profile_len.h
  • profile_mendelian.cpp
  • profile_mendelian.h
  • profile_na12878.cpp
  • profile_na12878.h
  • profile_snps.cpp
  • profile_snps.h
  • profile_vntrs.cpp
  • profile_vntrs.h
  • program.cpp
  • program.h
  • read_filter.cpp
  • read_filter.h
  • README.md
  • reference_sequence.cpp
  • reference_sequence.h
  • rfhmm.cpp
  • rfhmm.h
  • rfhmm_x.cpp
  • rfhmm_x.h
  • rminfo.cpp
  • rminfo.h
  • seq.cpp
  • seq.h
  • set_ref.cpp
  • set_ref.h
  • snp_genotyping_record.cpp
  • snp_genotyping_record.h
  • sort.cpp
  • sort.h
  • str_annotator.cpp
  • str_annotator.h
  • subset.cpp
  • subset.h
  • sv_tree.cpp
  • sv_tree.h
  • svm_predict.cpp
  • svm_predict.h
  • svm_train.cpp
  • svm_train.h
  • tbx_ordered_reader.cpp
  • tbx_ordered_reader.h
  • test.cpp
  • test.h
  • trio.cpp
  • trio.h
  • union_variants.cpp
  • union_variants.h
  • uniq.cpp
  • uniq.h
  • utils.cpp
  • utils.h
  • validate.cpp
  • validate.h
  • variant.cpp
  • variant.h
  • variant_filter.cpp
  • variant_filter.h
  • variant_manip.cpp
  • variant_manip.h
  • version.h
  • view.cpp
  • view.h
  • vntr.cpp
  • vntr.h
  • vntr_annotator.cpp
  • vntr_annotator.h
  • vntr_consolidator.cpp
  • vntr_consolidator.h
  • vntr_extractor.cpp
  • vntr_extractor.h
  • vntr_genotyping_record.cpp
  • vntr_genotyping_record.h
  • vntr_tree.cpp
  • vntr_tree.h
  • vntrize.cpp
  • vntrize.h
  • wdp_ahmm.cpp
  • wdp_ahmm.h

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