genetic-phasing-scripts

Collections of scripts for data generation and evaluation for Recomb-Seq 2022 submission: "Genetic Polyploid Phasing using Marker Signals from low-depth Progeny Samples"

Recreating ground truth region

Requires:

1. .gfa file containing the HiFi assemblies (ncbi)
2. Solyntus reference genome (public)
3. regions of parental VCF files (zenodo)

Run the snakemake pipeline Snakefile-ASM three times setting the chromosome variable to 3, 4 and 5 respectively.

Recreating the phasing results

Requires:

1. regions of parental VCF files (zenodo)
2. regions of progeny VCF files (zenodo)
3. ped files, specifying the pedigree relationships (zenodo)

Run the snakemake pipeline Snakefile-Genetic with rule all

If the downsampled parental coverage is to be reproduced as well, it requires: 4. regions of downsampled parental VCF files (zenodo)

Run the snakemake pipeline Snakefile-Genetic with rule downsample

Recreating the whole-chromosome results

Requires:

1. parental VCF files (ncbi)
2. progeny VCF files (ncbi)
3. ped file, specifying the pedigree relationships (zenodo)

Run the snakemake pipeline Snakefile-Whole.

Data availability

All files marked with either (zenodo), (public) or (ncbi), depending on whether the required data was uploaded on zenodo, is publicly available or available via an NCBI project. Please refer to the paper for further details. The NCBI data might be only available at a later point in time.

Link to Zenodo data: https://zenodo.org/record/5645743

Link to parental sequencing data: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA718240/

Link to progeny sequencing data: https://www.ncbi.nlm.nih.gov/bioproject/PRJEB48582/

Link to hifi read data for Altus: https://www.ncbi.nlm.nih.gov/sra/SUB10617521