├── .gitignore ├── .gitmodules ├── CHANGES.md ├── MERGE.md ├── README.md ├── Snakefile ├── TARGETS.md ├── files ├── .gitignore ├── filter │ ├── hg38 │ │ ├── all.bed │ │ ├── lc.bed │ │ └── lcy.bed │ └── mm10 │ │ └── all.bed ├── ref │ ├── GRCh37 │ │ ├── NOTES │ │ └── grc_report.tab │ └── GRCh38 │ │ ├── NOTES │ │ └── grc_report.tab └── tracks │ └── ucsc_track_fields.tsv ├── profiles ├── local │ └── config.yaml └── slurm │ └── config.yaml ├── rules ├── data │ ├── anno.snakefile │ ├── homopolymer.snakefile │ └── ref.snakefile ├── definitions.snakefile ├── flag │ ├── intersect.snakefile │ └── variant.snakefile ├── tracks │ └── variant.snakefile └── variant │ ├── anno │ ├── altmap.snakefile │ ├── homopolymer.snakefile │ ├── refseq.snakefile │ ├── regions.snakefile │ ├── regulation.snakefile │ ├── repeats.snakefile │ └── seq_content.snakefile │ ├── bed │ ├── altdup.snakefile │ ├── bed.snakefile │ ├── pavbed.snakefile │ ├── pavbedhap.snakefile │ ├── pbsv.snakefile │ ├── svim.snakefile │ └── vcf.snakefile │ ├── bedconversion.snakefile │ ├── callerset.snakefile │ ├── intersect.snakefile │ ├── intersect_nearest.snakefile │ ├── sampleset │ ├── anno.snakefile │ ├── bed.snakefile │ └── tables.snakefile │ ├── svset.snakefile │ ├── svtypecombined.snakefile │ ├── tables.snakefile │ ├── variant_global.snakefile │ └── vcf.snakefile ├── scripts └── filter_chrom.py └── svpoplib ├── __init__.py ├── aligner.py ├── anno ├── __init__.py └── align.py ├── callerset.py ├── constants.py ├── ds ├── __init__.py └── max_heap.py ├── gt.py ├── intersect.py ├── partition ├── __init__.py └── chrom.py ├── pd.py ├── plot ├── __init__.py ├── ideo.py ├── upset.py └── venn.py ├── ref.py ├── refseq.py ├── rules.py ├── sampleset.py ├── seq.py ├── sm.py ├── svlenoverlap.py ├── svmerge.py ├── svmergeconfig ├── __init__.py ├── lexer.py ├── params.py └── parser.py ├── svset.py ├── tracks ├── __init__.py └── variant.py ├── util.py ├── varbed.py ├── variant.py └── vcf.py /.gitignore: -------------------------------------------------------------------------------- 1 | svpoplib/**/__pycache__/ 2 | -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/.gitmodules -------------------------------------------------------------------------------- /CHANGES.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/CHANGES.md -------------------------------------------------------------------------------- /MERGE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/MERGE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/README.md -------------------------------------------------------------------------------- /Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/Snakefile -------------------------------------------------------------------------------- /TARGETS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/TARGETS.md -------------------------------------------------------------------------------- /files/.gitignore: -------------------------------------------------------------------------------- 1 | varset 2 | -------------------------------------------------------------------------------- /files/filter/hg38/all.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/files/filter/hg38/all.bed -------------------------------------------------------------------------------- /files/filter/hg38/lc.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/files/filter/hg38/lc.bed -------------------------------------------------------------------------------- /files/filter/hg38/lcy.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/files/filter/hg38/lcy.bed -------------------------------------------------------------------------------- /files/filter/mm10/all.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/files/filter/mm10/all.bed -------------------------------------------------------------------------------- /files/ref/GRCh37/NOTES: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/files/ref/GRCh37/NOTES -------------------------------------------------------------------------------- /files/ref/GRCh37/grc_report.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/files/ref/GRCh37/grc_report.tab -------------------------------------------------------------------------------- /files/ref/GRCh38/NOTES: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/files/ref/GRCh38/NOTES -------------------------------------------------------------------------------- /files/ref/GRCh38/grc_report.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/files/ref/GRCh38/grc_report.tab -------------------------------------------------------------------------------- /files/tracks/ucsc_track_fields.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/files/tracks/ucsc_track_fields.tsv -------------------------------------------------------------------------------- /profiles/local/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/profiles/local/config.yaml -------------------------------------------------------------------------------- /profiles/slurm/config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/profiles/slurm/config.yaml -------------------------------------------------------------------------------- /rules/data/anno.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/data/anno.snakefile -------------------------------------------------------------------------------- /rules/data/homopolymer.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/data/homopolymer.snakefile -------------------------------------------------------------------------------- /rules/data/ref.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/data/ref.snakefile -------------------------------------------------------------------------------- /rules/definitions.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/definitions.snakefile -------------------------------------------------------------------------------- /rules/flag/intersect.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/flag/intersect.snakefile -------------------------------------------------------------------------------- /rules/flag/variant.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/flag/variant.snakefile -------------------------------------------------------------------------------- /rules/tracks/variant.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/tracks/variant.snakefile -------------------------------------------------------------------------------- /rules/variant/anno/altmap.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/anno/altmap.snakefile -------------------------------------------------------------------------------- /rules/variant/anno/homopolymer.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/anno/homopolymer.snakefile -------------------------------------------------------------------------------- /rules/variant/anno/refseq.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/anno/refseq.snakefile -------------------------------------------------------------------------------- /rules/variant/anno/regions.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/anno/regions.snakefile -------------------------------------------------------------------------------- /rules/variant/anno/regulation.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/anno/regulation.snakefile -------------------------------------------------------------------------------- /rules/variant/anno/repeats.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/anno/repeats.snakefile -------------------------------------------------------------------------------- /rules/variant/anno/seq_content.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/anno/seq_content.snakefile -------------------------------------------------------------------------------- /rules/variant/bed/altdup.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/bed/altdup.snakefile -------------------------------------------------------------------------------- /rules/variant/bed/bed.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/bed/bed.snakefile -------------------------------------------------------------------------------- /rules/variant/bed/pavbed.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/bed/pavbed.snakefile -------------------------------------------------------------------------------- /rules/variant/bed/pavbedhap.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/bed/pavbedhap.snakefile -------------------------------------------------------------------------------- /rules/variant/bed/pbsv.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/bed/pbsv.snakefile -------------------------------------------------------------------------------- /rules/variant/bed/svim.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/bed/svim.snakefile -------------------------------------------------------------------------------- /rules/variant/bed/vcf.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/bed/vcf.snakefile -------------------------------------------------------------------------------- /rules/variant/bedconversion.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/bedconversion.snakefile -------------------------------------------------------------------------------- /rules/variant/callerset.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/callerset.snakefile -------------------------------------------------------------------------------- /rules/variant/intersect.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/intersect.snakefile -------------------------------------------------------------------------------- /rules/variant/intersect_nearest.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/intersect_nearest.snakefile -------------------------------------------------------------------------------- /rules/variant/sampleset/anno.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/sampleset/anno.snakefile -------------------------------------------------------------------------------- /rules/variant/sampleset/bed.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/sampleset/bed.snakefile -------------------------------------------------------------------------------- /rules/variant/sampleset/tables.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/sampleset/tables.snakefile -------------------------------------------------------------------------------- /rules/variant/svset.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/svset.snakefile -------------------------------------------------------------------------------- /rules/variant/svtypecombined.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/svtypecombined.snakefile -------------------------------------------------------------------------------- /rules/variant/tables.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/tables.snakefile -------------------------------------------------------------------------------- /rules/variant/variant_global.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/variant_global.snakefile -------------------------------------------------------------------------------- /rules/variant/vcf.snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/rules/variant/vcf.snakefile -------------------------------------------------------------------------------- /scripts/filter_chrom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/scripts/filter_chrom.py -------------------------------------------------------------------------------- /svpoplib/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/__init__.py -------------------------------------------------------------------------------- /svpoplib/aligner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/aligner.py -------------------------------------------------------------------------------- /svpoplib/anno/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/anno/__init__.py -------------------------------------------------------------------------------- /svpoplib/anno/align.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/anno/align.py -------------------------------------------------------------------------------- /svpoplib/callerset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/callerset.py -------------------------------------------------------------------------------- /svpoplib/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/constants.py -------------------------------------------------------------------------------- /svpoplib/ds/__init__.py: -------------------------------------------------------------------------------- 1 | __all__ = [] 2 | 3 | from . import max_heap 4 | -------------------------------------------------------------------------------- /svpoplib/ds/max_heap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/ds/max_heap.py -------------------------------------------------------------------------------- /svpoplib/gt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/gt.py -------------------------------------------------------------------------------- /svpoplib/intersect.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/intersect.py -------------------------------------------------------------------------------- /svpoplib/partition/__init__.py: -------------------------------------------------------------------------------- 1 | __all__ = [] 2 | 3 | from . import chrom -------------------------------------------------------------------------------- /svpoplib/partition/chrom.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/partition/chrom.py -------------------------------------------------------------------------------- /svpoplib/pd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/pd.py -------------------------------------------------------------------------------- /svpoplib/plot/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/plot/__init__.py -------------------------------------------------------------------------------- /svpoplib/plot/ideo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/plot/ideo.py -------------------------------------------------------------------------------- /svpoplib/plot/upset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/plot/upset.py -------------------------------------------------------------------------------- /svpoplib/plot/venn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/plot/venn.py -------------------------------------------------------------------------------- /svpoplib/ref.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/ref.py -------------------------------------------------------------------------------- /svpoplib/refseq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/refseq.py -------------------------------------------------------------------------------- /svpoplib/rules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/rules.py -------------------------------------------------------------------------------- /svpoplib/sampleset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/sampleset.py -------------------------------------------------------------------------------- /svpoplib/seq.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/seq.py -------------------------------------------------------------------------------- /svpoplib/sm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/sm.py -------------------------------------------------------------------------------- /svpoplib/svlenoverlap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/svlenoverlap.py -------------------------------------------------------------------------------- /svpoplib/svmerge.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/svmerge.py -------------------------------------------------------------------------------- /svpoplib/svmergeconfig/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/svmergeconfig/__init__.py -------------------------------------------------------------------------------- /svpoplib/svmergeconfig/lexer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/svmergeconfig/lexer.py -------------------------------------------------------------------------------- /svpoplib/svmergeconfig/params.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/svmergeconfig/params.py -------------------------------------------------------------------------------- /svpoplib/svmergeconfig/parser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/svmergeconfig/parser.py -------------------------------------------------------------------------------- /svpoplib/svset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/svset.py -------------------------------------------------------------------------------- /svpoplib/tracks/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/tracks/__init__.py -------------------------------------------------------------------------------- /svpoplib/tracks/variant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/tracks/variant.py -------------------------------------------------------------------------------- /svpoplib/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/util.py -------------------------------------------------------------------------------- /svpoplib/varbed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/varbed.py -------------------------------------------------------------------------------- /svpoplib/variant.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/variant.py -------------------------------------------------------------------------------- /svpoplib/vcf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/EichlerLab/svpop/HEAD/svpoplib/vcf.py --------------------------------------------------------------------------------