├── .gitignore ├── LICENSE ├── README.md ├── benchmarks └── gatk │ ├── HG002+HG003+HG004.NovaSeq.100x.hs38DH.bwa.dedup.tsv │ ├── HG002+HG003+HG004.NovaSeq.10x.hs38DH.bwa.dedup.tsv │ ├── HG002+HG003+HG004.NovaSeq.20x.hs38DH.bwa.dedup.tsv │ ├── HG002+HG003+HG004.NovaSeq.30x.hs38DH.bwa.dedup.tsv │ ├── HG002+HG003+HG004.NovaSeq.40x.hs38DH.bwa.dedup.tsv │ ├── HG002+HG003+HG004.NovaSeq.50x.hs38DH.bwa.dedup.tsv │ ├── HG002+HG003+HG004.NovaSeq.60x.hs38DH.bwa.dedup.tsv │ ├── HG002+HG003+HG004.NovaSeq.70x.hs38DH.bwa.dedup.tsv │ ├── HG002+HG003+HG004.NovaSeq.80x.hs38DH.bwa.dedup.tsv │ ├── HG002+HG003+HG004.NovaSeq.90x.hs38DH.bwa.dedup.tsv │ ├── HG002.NovaSeq.10x.hs38DH.bwa.dedup.tsv │ ├── HG002.NovaSeq.20x.hs38DH.bwa.dedup.tsv │ ├── HG002.NovaSeq.30x.hs38DH.bwa.dedup.tsv │ ├── HG003+HG004.NovaSeq.10x.hs38DH.bwa.dedup.tsv │ ├── HG003+HG004.NovaSeq.20x.hs38DH.bwa.dedup.tsv │ ├── HG003+HG004.NovaSeq.30x.hs38DH.bwa.dedup.tsv │ ├── HG003+HG004.NovaSeq.40x.hs38DH.bwa.dedup.tsv │ ├── HG003+HG004.NovaSeq.50x.hs38DH.bwa.dedup.tsv │ ├── HG003+HG004.NovaSeq.60x.hs38DH.bwa.dedup.tsv │ ├── HG003+HG004.NovaSeq.70x.hs38DH.bwa.dedup.tsv │ ├── banana.HiSeq.55x.musa_acuminata.bwa.dedup.tsv │ └── banana.NextSeq.65x.musa_acuminata.bwa.dedup.tsv ├── config ├── banana.yaml ├── diploid_novaseq.yaml ├── diploid_pacbio.yaml ├── hexaploid_novaseq.yaml ├── hexaploid_pacbio.yaml ├── tetraploid_novaseq.yaml ├── tetraploid_novaseq_example.yaml ├── tetraploid_novaseq_longhaps.yaml └── tetraploid_pacbio.yaml ├── paper ├── main │ ├── figures │ │ ├── accuracies-by-depth.pdf │ │ ├── banana_intersections.pdf │ │ ├── hexaploid_gt_fn_perc_10x_50x_100x.pdf │ │ ├── hexaploid_gt_fp_10x_50x_100x.pdf │ │ ├── synthetic-tetraploid-pr-curves_20-50x.pdf │ │ ├── tetraploid_haplotypes.png │ │ └── tetraploid_haplotypes.svg │ ├── main.pdf │ ├── main.tex │ └── references.bib └── supplementary │ ├── figures │ ├── accuracies-by-depth-alleles.pdf │ ├── banana_intersections_alleles.pdf │ ├── hexaploid_biallelic_copy_errors.pdf │ ├── hexaploid_gt_fn.pdf │ ├── hexaploid_gt_fn_perc.pdf │ ├── hexaploid_gt_fp.pdf │ ├── synthetic-hexaploid-pr-curves.pdf │ ├── synthetic-tetraploid-pr-curves.pdf │ ├── tetraploid_biallelic_copy_errors.pdf │ ├── tetraploid_gt_fn.pdf │ ├── tetraploid_gt_fn_perc.pdf │ └── tetraploid_gt_fp.pdf │ ├── supplementary.bib │ ├── supplementary.pdf │ ├── supplementary.tex │ └── tables │ ├── supp_table1.xlsx │ ├── supp_table2.xlsx │ └── supp_table3.xlsx └── workflow ├── Snakefile ├── envs ├── bedtools.yaml ├── bwa.yaml ├── bwakit.yaml ├── freebayes.yaml ├── gatk4.yaml ├── octopus.yaml ├── pbmm2.yaml ├── rtg.yaml ├── samtools.yaml └── seqtk.yaml ├── notebooks ├── .ipynb_checkpoints │ └── benchmark.py-checkpoint.ipynb └── benchmark.py.ipynb ├── rules ├── data.smk ├── evaluate.smk ├── freebayes.smk ├── gatk.smk ├── mapping.smk ├── octopus.smk └── utils.smk └── scripts ├── gatk_parallel.py ├── starfish.py └── vcfeval.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/README.md -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.100x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.100x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.10x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.10x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.20x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.20x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.30x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.30x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.40x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.40x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.50x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.50x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.60x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.60x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.70x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.70x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.80x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.80x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002+HG003+HG004.NovaSeq.90x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002+HG003+HG004.NovaSeq.90x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002.NovaSeq.10x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002.NovaSeq.10x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002.NovaSeq.20x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002.NovaSeq.20x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG002.NovaSeq.30x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG002.NovaSeq.30x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG003+HG004.NovaSeq.10x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG003+HG004.NovaSeq.10x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG003+HG004.NovaSeq.20x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG003+HG004.NovaSeq.20x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG003+HG004.NovaSeq.30x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG003+HG004.NovaSeq.30x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG003+HG004.NovaSeq.40x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG003+HG004.NovaSeq.40x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG003+HG004.NovaSeq.50x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG003+HG004.NovaSeq.50x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG003+HG004.NovaSeq.60x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG003+HG004.NovaSeq.60x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/HG003+HG004.NovaSeq.70x.hs38DH.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/HG003+HG004.NovaSeq.70x.hs38DH.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/banana.HiSeq.55x.musa_acuminata.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/banana.HiSeq.55x.musa_acuminata.bwa.dedup.tsv -------------------------------------------------------------------------------- /benchmarks/gatk/banana.NextSeq.65x.musa_acuminata.bwa.dedup.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/benchmarks/gatk/banana.NextSeq.65x.musa_acuminata.bwa.dedup.tsv -------------------------------------------------------------------------------- /config/banana.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/config/banana.yaml -------------------------------------------------------------------------------- /config/diploid_novaseq.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/config/diploid_novaseq.yaml -------------------------------------------------------------------------------- /config/diploid_pacbio.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/config/diploid_pacbio.yaml -------------------------------------------------------------------------------- /config/hexaploid_novaseq.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/config/hexaploid_novaseq.yaml -------------------------------------------------------------------------------- /config/hexaploid_pacbio.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/config/hexaploid_pacbio.yaml -------------------------------------------------------------------------------- /config/tetraploid_novaseq.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/config/tetraploid_novaseq.yaml -------------------------------------------------------------------------------- /config/tetraploid_novaseq_example.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/config/tetraploid_novaseq_example.yaml -------------------------------------------------------------------------------- /config/tetraploid_novaseq_longhaps.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/config/tetraploid_novaseq_longhaps.yaml -------------------------------------------------------------------------------- /config/tetraploid_pacbio.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/config/tetraploid_pacbio.yaml -------------------------------------------------------------------------------- /paper/main/figures/accuracies-by-depth.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/figures/accuracies-by-depth.pdf -------------------------------------------------------------------------------- /paper/main/figures/banana_intersections.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/figures/banana_intersections.pdf -------------------------------------------------------------------------------- /paper/main/figures/hexaploid_gt_fn_perc_10x_50x_100x.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/figures/hexaploid_gt_fn_perc_10x_50x_100x.pdf -------------------------------------------------------------------------------- /paper/main/figures/hexaploid_gt_fp_10x_50x_100x.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/figures/hexaploid_gt_fp_10x_50x_100x.pdf -------------------------------------------------------------------------------- /paper/main/figures/synthetic-tetraploid-pr-curves_20-50x.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/figures/synthetic-tetraploid-pr-curves_20-50x.pdf -------------------------------------------------------------------------------- /paper/main/figures/tetraploid_haplotypes.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/figures/tetraploid_haplotypes.png -------------------------------------------------------------------------------- /paper/main/figures/tetraploid_haplotypes.svg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/figures/tetraploid_haplotypes.svg -------------------------------------------------------------------------------- /paper/main/main.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/main.pdf -------------------------------------------------------------------------------- /paper/main/main.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/main.tex -------------------------------------------------------------------------------- /paper/main/references.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/main/references.bib -------------------------------------------------------------------------------- /paper/supplementary/figures/accuracies-by-depth-alleles.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/accuracies-by-depth-alleles.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/banana_intersections_alleles.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/banana_intersections_alleles.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/hexaploid_biallelic_copy_errors.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/hexaploid_biallelic_copy_errors.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/hexaploid_gt_fn.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/hexaploid_gt_fn.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/hexaploid_gt_fn_perc.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/hexaploid_gt_fn_perc.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/hexaploid_gt_fp.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/hexaploid_gt_fp.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/synthetic-hexaploid-pr-curves.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/synthetic-hexaploid-pr-curves.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/synthetic-tetraploid-pr-curves.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/synthetic-tetraploid-pr-curves.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/tetraploid_biallelic_copy_errors.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/tetraploid_biallelic_copy_errors.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/tetraploid_gt_fn.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/tetraploid_gt_fn.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/tetraploid_gt_fn_perc.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/tetraploid_gt_fn_perc.pdf -------------------------------------------------------------------------------- /paper/supplementary/figures/tetraploid_gt_fp.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/figures/tetraploid_gt_fp.pdf -------------------------------------------------------------------------------- /paper/supplementary/supplementary.bib: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/supplementary.bib -------------------------------------------------------------------------------- /paper/supplementary/supplementary.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/supplementary.pdf -------------------------------------------------------------------------------- /paper/supplementary/supplementary.tex: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/supplementary.tex -------------------------------------------------------------------------------- /paper/supplementary/tables/supp_table1.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/tables/supp_table1.xlsx -------------------------------------------------------------------------------- /paper/supplementary/tables/supp_table2.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/tables/supp_table2.xlsx -------------------------------------------------------------------------------- /paper/supplementary/tables/supp_table3.xlsx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/paper/supplementary/tables/supp_table3.xlsx -------------------------------------------------------------------------------- /workflow/Snakefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/Snakefile -------------------------------------------------------------------------------- /workflow/envs/bedtools.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/bedtools.yaml -------------------------------------------------------------------------------- /workflow/envs/bwa.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/bwa.yaml -------------------------------------------------------------------------------- /workflow/envs/bwakit.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/bwakit.yaml -------------------------------------------------------------------------------- /workflow/envs/freebayes.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/freebayes.yaml -------------------------------------------------------------------------------- /workflow/envs/gatk4.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/gatk4.yaml -------------------------------------------------------------------------------- /workflow/envs/octopus.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/octopus.yaml -------------------------------------------------------------------------------- /workflow/envs/pbmm2.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/pbmm2.yaml -------------------------------------------------------------------------------- /workflow/envs/rtg.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/rtg.yaml -------------------------------------------------------------------------------- /workflow/envs/samtools.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/samtools.yaml -------------------------------------------------------------------------------- /workflow/envs/seqtk.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/envs/seqtk.yaml -------------------------------------------------------------------------------- /workflow/notebooks/.ipynb_checkpoints/benchmark.py-checkpoint.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/notebooks/.ipynb_checkpoints/benchmark.py-checkpoint.ipynb -------------------------------------------------------------------------------- /workflow/notebooks/benchmark.py.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/notebooks/benchmark.py.ipynb -------------------------------------------------------------------------------- /workflow/rules/data.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/rules/data.smk -------------------------------------------------------------------------------- /workflow/rules/evaluate.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/rules/evaluate.smk -------------------------------------------------------------------------------- /workflow/rules/freebayes.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/rules/freebayes.smk -------------------------------------------------------------------------------- /workflow/rules/gatk.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/rules/gatk.smk -------------------------------------------------------------------------------- /workflow/rules/mapping.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/rules/mapping.smk -------------------------------------------------------------------------------- /workflow/rules/octopus.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/rules/octopus.smk -------------------------------------------------------------------------------- /workflow/rules/utils.smk: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/rules/utils.smk -------------------------------------------------------------------------------- /workflow/scripts/gatk_parallel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/scripts/gatk_parallel.py -------------------------------------------------------------------------------- /workflow/scripts/starfish.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/scripts/starfish.py -------------------------------------------------------------------------------- /workflow/scripts/vcfeval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/luntergroup/polyploid/HEAD/workflow/scripts/vcfeval.py --------------------------------------------------------------------------------