GitHub - EichlerLab/ssf_DTS_caller: scale space filtering based CNV calling and genotyping

#ssf_DTS_caller

ssf_DTS_caller is a package for calling CNVs from read-depth illumina data. The package has a number of dependencies, including, DenseTrackSets, and DTS genotype files. It also contains genotype_regions, a simple utility for getting genotypes for a set of regions.

Name		Name	Last commit message	Last commit date
Latest commit History 275 Commits
heap		heap
.gitignore		.gitignore
GC_data.py		GC_data.py
Makefile		Makefile
README.md		README.md
__init__.py		__init__.py
bw_builder.py		bw_builder.py
c_hierarchical_edge_merge.pyx		c_hierarchical_edge_merge.pyx
cluster.py		cluster.py
compile_note.txt		compile_note.txt
edge.cc		edge.cc
edge.h		edge.h
edge_cluster.py		edge_cluster.py
filter_VCF.py		filter_VCF.py
filter_to_simple_gts.py		filter_to_simple_gts.py
float_heap.cc		float_heap.cc
genotype_refined_call_sets.py		genotype_refined_call_sets.py
genotype_regions.py		genotype_regions.py
genotyper.py		genotyper.py
get_gc_cp2_stats.py		get_gc_cp2_stats.py
get_windowed_variance.pyx		get_windowed_variance.pyx
gglob.py		gglob.py
gglob_genotyper.py		gglob_genotyper.py
info_io.py		info_io.py
line_plot.py		line_plot.py
make_dCGH_calls.py		make_dCGH_calls.py
merge_individual_tables.py		merge_individual_tables.py
merge_individual_tables.sh		merge_individual_tables.sh
merge_individual_tables_by_indiv.sh		merge_individual_tables_by_indiv.sh
modules.sh		modules.sh
null_distribution.py		null_distribution.py
plot.py		plot.py
refine_calls.py		refine_calls.py
setup.py		setup.py
simple_genotyper.py		simple_genotyper.py
ssf_caller.py		ssf_caller.py
super_sorter.py		super_sorter.py
test_G_overlap.py		test_G_overlap.py
traverse_contours.pyx		traverse_contours.pyx
wnd_cp_data.py		wnd_cp_data.py

EichlerLab/ssf_DTS_caller

Folders and files

Latest commit

History

Repository files navigation

About

Resources

Stars

Watchers

Forks

Languages