SWIM analysis and server codes

The codes are largely organized based on programming languages. The main workflows are always programmed using bash scripts, which may call additional bash, SLURM sbatch (for use on a cluster), R, or perl scripts.

Construction and evaluation of the haplotype reference panel

1. prepare sequence files

codes in (bash/prepSeq.bash), which includes downloading and processing SRA sequences to conform to formats (directory structures, file names) that are compatible with downstream steps.

2. mapping, post-mapping processing, and call variants in GVCF

codes in (bash/gvcfs.bash) which calls (bash/fq2gvcf.bash).

3. combine GVCFs and genotype GVCFs

codes in (bash/combineGenotype.bash) and (bash/genotype.bash), including variant quality recalibration.

4. QC, filtering

codes in (bash/QC.bash).

5. evaluation of imputation software combinations, reference panel composition

codes in (bash/acc_ind550_imputation.bash)

SWIM server

codes in the directory (server/)

Figures

codes in the directory (figureCode/) and data needed to generate the figures in (figureData/)