The repository hosts the snakemake pipelines and analysis scripts used for analysing the 1,019 samples sequenced with ONT long-reads.
The following snakemake pipelines are hosted in this repository:
- Haplotagging of Aligned Reads under
haplotagging: The pipeline tags the aligned reads of this study as originating from haplotype 1 or 2 usingwhatshap. - Phasing Experiments under
phasing: The pipeline phases the NYGC raw genotyes using the aligned reads withwhatshapand we perform QC using the NYGC statistical phased VCF. - Running Giggles and SVarp on the HPRC_mg graph under
pre-augmentation-giggles-svarp: The pipeline pre-processes and does SV discovery withSVarpand SV genotyping withgigglesusing HPRC_mg. - Running Giggles on the HPRC_mg_44+966 graph under
post-augmentation-genotyping: The pipeline pre-processes and does SV genotyping withgigglesusing HPRC_mg_44+966. - Running QCs based on coverage and read N50 stratification under
genotype-sample-subet-analysis: The pipeline bins the samples based on coverage and read N50 and runs QC to check the effects of these two variables on genotyping and SV discovery. - Investigating recovery of added SVs during genotyping under
sv-recovery: The pipeline investigates the SVs that were introduced into the graph to create HPRC_mg_44+966 and whether they were retrieved during genotyping. - Annotating the alleles in HPRC_mg_44+966 based on the ancestral allele found in Chimpanzee under
chimpanzee-analysis: The pipeline identifies ancestral allele in the chimpanzee using alignment of the chimpanzee assembly to HPRC_mg_44+966 and tags the VCFs produced fromgiggles. - VNTR genotyping of the cohort using vamos under
vamos-analysis: The pipeline runs the VNTR calling usingvamosand subsequent QC with the HGSVC3 assemblies.
For information about the other scripts, please refer to the "Code Availability" section of the preprint.
Link to preprint: https://www.biorxiv.org/content/10.1101/2024.04.18.590093v1