├── .gitignore ├── .gitmodules ├── LICENSE ├── README.md ├── resources ├── 1kg.superpopulation ├── 1kgp.indiv_population ├── GRCh38.chrom_map └── GRCh38.length_map ├── snakemake ├── README.md ├── Snakefile ├── config.yaml └── shared │ ├── alignment_paired_end.Snakefile │ ├── alignment_single_end.Snakefile │ ├── functions.Snakefile │ ├── lift_and_sort.Snakefile │ ├── prepare_pop_genome.Snakefile │ └── prepare_standard_genome.Snakefile ├── src ├── Makefile ├── add_aux.cpp ├── add_aux.hpp ├── download_1kg_pop_table.sh ├── download_1kg_vcf.sh ├── download_genome.sh ├── download_prebuilt_indexes.sh ├── list_indiv_from_pop.py ├── merge_incremental.py ├── merge_sam.cpp ├── merge_sam.hpp ├── refflow_utils.cpp ├── refflow_utils.hpp ├── split_sam.cpp ├── split_sam.hpp ├── split_sam_by_mapq.py ├── update_genome.py └── utils.py └── test └── SRR622457_1-1k.fastq /.gitignore: -------------------------------------------------------------------------------- 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