Name		Name	Last commit message	Last commit date
Latest commit History 143 Commits
HapCUT2 @ d04e51b		HapCUT2 @ d04e51b
envs		envs
genome_tracks		genome_tracks
map_counter		map_counter
notebooks		notebooks
scripts		scripts
.gitignore		.gitignore
.gitmodules		.gitmodules
LICENSE		LICENSE
NA12878.1000g.snakefile		NA12878.1000g.snakefile
NA12878.hg38.snakefile		NA12878.hg38.snakefile
NA24143.1000g.snakefile		NA24143.1000g.snakefile
NA24143.hg38.snakefile		NA24143.hg38.snakefile
NA24149.1000g.snakefile		NA24149.1000g.snakefile
NA24149.hg38.snakefile		NA24149.hg38.snakefile
NA24385.1000g.snakefile		NA24385.1000g.snakefile
NA24385.hg38.snakefile		NA24385.hg38.snakefile
README.md		README.md
Snakefile		Snakefile
aj-trio.ped		aj-trio.ped
aj_trio.snakefile		aj_trio.snakefile
analyze_variants.py		analyze_variants.py
calculate_coverage.py		calculate_coverage.py
cluster.yaml		cluster.yaml
convert_fastq_to_pacbio_fasta.py		convert_fastq_to_pacbio_fasta.py
duplicated_gene_visualization.snakefile		duplicated_gene_visualization.snakefile
filter_SNVs.py		filter_SNVs.py
filter_bed_chroms.py		filter_bed_chroms.py
filter_quadrallelic_sites.py		filter_quadrallelic_sites.py
haplotyping.snakefile		haplotyping.snakefile
intersect_SNV_genotypes.py		intersect_SNV_genotypes.py
longshot_study_environment.yml		longshot_study_environment.yml
make_duplicated_gene_table.snakefile		make_duplicated_gene_table.snakefile
make_variant_counts_table.snakefile		make_variant_counts_table.snakefile
make_variant_counts_table_GIAB.snakefile		make_variant_counts_table_GIAB.snakefile
map_giab_reads.snakefile		map_giab_reads.snakefile
mapping_accuracy.py		mapping_accuracy.py
merge_phasedvcfs.py		merge_phasedvcfs.py
paper_tables_and_figures.py		paper_tables_and_figures.py
paper_tables_and_figures.snakefile		paper_tables_and_figures.snakefile
plot_precision_recall_bars.py		plot_precision_recall_bars.py
replace_empty_gt_with_reference.py		replace_empty_gt_with_reference.py
run_pileups.py		run_pileups.py
sequence.index.AJtrio_PacBio_MtSinai_NIST_hdf5_08072015.txt		sequence.index.AJtrio_PacBio_MtSinai_NIST_hdf5_08072015.txt
simulate_SNVs.py		simulate_SNVs.py
simulation.1000g.snakefile		simulation.1000g.snakefile

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longshot_study

This repository contains a Snakemake recipe to recreate the Longshot study

Most of the required programs are contained in the conda environment described by longshot_study_environment.yml.

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pjedge/longshot_study

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longshot_study

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