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

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lib/include
lib/include
 
 
LICENSE
LICENSE
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
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
 
 
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
 
 
compute_concordance.cpp
compute_concordance.cpp
 
 
compute_concordance.h
compute_concordance.h
 
 
concat.cpp
concat.cpp
 
 
concat.h
concat.h
 
 
construct_probes.cpp
construct_probes.cpp
 
 
construct_probes.h
construct_probes.h
 
 
decompose.cpp
decompose.cpp
 
 
decompose.h
decompose.h
 
 
discover.cpp
discover.cpp
 
 
discover.h
discover.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
 
 
genotyping_buffer.cpp
genotyping_buffer.cpp
 
 
genotyping_buffer.h
genotyping_buffer.h
 
 
genotyping_record.cpp
genotyping_record.cpp
 
 
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_tree.cpp
interval_tree.cpp
 
 
interval_tree.h
interval_tree.h
 
 
lhmm.cpp
lhmm.cpp
 
 
lhmm.h
lhmm.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
 
 
merge_duplicate_variants.cpp
merge_duplicate_variants.cpp
 
 
merge_duplicate_variants.h
merge_duplicate_variants.h
 
 
normalize.cpp
normalize.cpp
 
 
normalize.h
normalize.h
 
 
partition.cpp
partition.cpp
 
 
partition.h
partition.h
 
 
pedigree.cpp
pedigree.cpp
 
 
pedigree.h
pedigree.h
 
 
peek.cpp
peek.cpp
 
 
peek.h
peek.h
 
 
profile_indels.cpp
profile_indels.cpp
 
 
profile_indels.h
profile_indels.h
 
 
profile_mendelian.cpp
profile_mendelian.cpp
 
 
profile_mendelian.h
profile_mendelian.h
 
 
profile_na12878.cpp
profile_na12878.cpp
 
 
profile_na12878.h
profile_na12878.h
 
 
profile_snps.cpp
profile_snps.cpp
 
 
profile_snps.h
profile_snps.h
 
 
program.cpp
program.cpp
 
 
program.h
program.h
 
 
remove_overlap.cpp
remove_overlap.cpp
 
 
remove_overlap.h
remove_overlap.h
 
 
tbx_ordered_reader.cpp
tbx_ordered_reader.cpp
 
 
tbx_ordered_reader.h
tbx_ordered_reader.h
 
 
utils.cpp
utils.cpp
 
 
utils.h
utils.h
 
 
variant_manip.cpp
variant_manip.cpp
 
 
variant_manip.h
variant_manip.h
 
 
view.cpp
view.cpp
 
 
view.h
view.h
 
 

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

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