Bioinfor-wf-nipt-human-genetics

Overview

Bioinfor-wf-nipt-human-genetics is an end-to-end NIPT (Non-Invasive Prenatal Testing) GWAS (Genome-Wide Association Study) pipeline designed for processing fastq files. This pipeline facilitates the analysis of human genetics for NIPT applications and can be easily adapted for various research scenarios.

This one is the effort to reproduce the analysis on the below studies using nextflow and large scale cluster:

1. Liu, S., Liu, Y., Gu, Y., Lin, X., Zhu, H., Liu, H., Xu, Z., Cheng, S., Lan, X., Li, L. and Huang, M., 2024. Utilizing non-invasive prenatal test sequencing data for human genetic investigation. Cell Genomics, 4(10)
2. Zeng, J., Li, L., Lin, Y., Lan, X., Zhang, X., Wang, Y., Liao, M., Jin, X. and Zhu, H., 2025. Protocol for genetic analysis of population-scale ultra-low-depth sequencing data. STAR protocols, 6(1), p.103579.
3. Xiao, H., Li, L., Yang, M., Zhang, X., Zhou, J., Zeng, J., Zhou, Y., Lan, X., Liu, J., Lin, Y. and Zhong, Y., 2024. Genetic analyses of 104 phenotypes in 20,900 Chinese pregnant women reveal pregnancy-specific discoveries. Cell Genomics, 4(10).

Key Features

End-to-end workflow for processing fastq files into NIPT GWAS results.

Designed to handle more than 50 samples for real-world applications.

Collects necessary parameters for easy configuration.

Simplifies the creation of test profiles for easy setup and execution.

Usages

Install river-utils:

Install micromamba and river-utils

version="v1.2.0"
bash <(curl -Ls https://raw.githubusercontent.com/riverxdata/river-utils/${version}/install/setup.sh) $HOME $version
source ~/.river.sh

Check required softwares

which nextflow
which singularity
# examples
# /home/river/.river/images/micromamba/envs/river/bin/nextflow
# /home/river/.river/images/micromamba/envs/river/bin/singularity

Setup

Get latest workflow

git clone https://github.com/riverxdata/bioinfor-wf-nipt-human-genetics
cd bioinfor-wf-nipt-human-genetics

Prepare the reference genome and database

# gcs 1KPG with known variants db and reference genomes
micromamba install conda-forge::google-cloud-sdk
mkdir -p data/gcs
gsutil -m cp -r \
  "gs://genomics-public-data/resources/broad/hg38/v0/1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf" \
  "gs://genomics-public-data/resources/broad/hg38/v0/1000G.phase3.integrated.sites_only.no_MATCHED_REV.hg38.vcf.idx" \
  "gs://genomics-public-data/resources/broad/hg38/v0/1000G_omni2.5.hg38.vcf.gz" \
  "gs://genomics-public-data/resources/broad/hg38/v0/1000G_omni2.5.hg38.vcf.gz.tbi" \
  "gs://genomics-public-data/resources/broad/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz" \
  "gs://genomics-public-data/resources/broad/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.dict" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.alt" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.amb" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.ann" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.bwt" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.pac" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.64.sa" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta.fai" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz" \
  "gs://genomics-public-data/resources/broad/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi" \
  "gs://genomics-public-data/resources/broad/hg38/v0/hapmap_3.3.hg38.vcf.gz" \
  "gs://genomics-public-data/resources/broad/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi" \
  "gs://genomics-public-data/resources/broad/hg38/v0/scattered_calling_intervals" \
  "gs://genomics-public-data/resources/broad/hg38/v0/wgs_calling_regions.hg38.interval_list" \
  .
# gmap files
cd ..
mkdir -p gmap && cd gmap
git clone https://github.com/odelaneau/GLIMPSE.git

# phasing db
cd ..
mkdir -p phasing && cd phasing
# example to run on small chromosomes
for i in {21..22}
do
    wget -c http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/CCDG_14151_B01_GRM_WGS_2020-08-05_chr$i.filtered.shapeit2-duohmm-phased.vcf.gz
    wget -c http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20201028_3202_phased/CCDG_14151_B01_GRM_WGS_2020-08-05_chr$i.filtered.shapeit2-duohmm-phased.vcf.gz.tbi
done

Data

Open this on your browser, https://zenodo.org/records/13382182 Download and unzip in the data folder

data
├── gcs
├── gmap
├── gwas
├── phasing
└── samples
    ├── CL10001L0250.fq.gz
    ├── CL10002L0141.fq.gz
    ├── CL10003L0260.fq.gz
    ├── CL10004L0265.fq.gz
    ├── CL10005L0280.fq.gz
    ├── CL10006L0260.fq.gz
    ├── CL10007L0165.fq.gz
    ├── CL10008L0241.fq.gz
    ├── CL10009L0160.fq.gz
    ├── CL10010L0282.fq.gz
    ├── files-archive
    ├── fq.list
    └── sample.csv

Execute the pipeline

nextflow run main.nf -profile docker -resume --outdir result
# Launching `main.nf` [insane_franklin] DSL2 - revision: cea5343a10

# ================== Pipeline Parameters =======================================================
# Input file:                 /home/river/bioinfor-wf-nipt/data/samples/fq.list
# Phenotype file:            /home/river/bioinfor-wf-nipt/data/gwas/phenotype.txt
# Reference genome:          /home/river/bioinfor-wf-nipt/data/gcs/Homo_sapiens_assembly38
# 1k Gold Indel DB:          /home/river/bioinfor-wf-nipt/data/gcs/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
# Known Assembly Indel DB:   /home/river/bioinfor-wf-nipt/data/gcs/Homo_sapiens_assembly38.known_indels.vcf.gz
# dbSNP DB:                  /home/river/bioinfor-wf-nipt/data/gcs/Homo_sapiens_assembly38.dbsnp138.vcf
# Genetic Maps:              /home/river/bioinfor-wf-nipt/data/gmap/GLIMPSE/maps/genetic_maps.b38
# Reference Panel DB:        /home/river/bioinfor-wf-nipt/data/phasing
# ==============================================================================================
# Workflow maintained by Thanh-Giang (River) Tan Nguyen
# For inquiries, contact: giangnguyen@riverxdata.com