Workflow for analysis of nanopore amplicon sequencing data to genotype variants in the G6PD, HBB, and ACKR1 (Duffy) genes, as well as the Dantu variant.
Lab assay methods adapted from https://pubmed.ncbi.nlm.nih.gov/37495620/
Analysis scripts adapted from https://github.com/LSHTMPathogenSeqLab/amplicon-seq/tree/main and https://github.com/sophiemoss/smoss_ampseq/tree/main
Follow run_pipeline.sh
- Bed file: GRCh38_amplicon_targets_updated_sorted.bed
- Bed file with numeric chromosomes: GRCh38_amplicon_targets_updated_sorted_num.bed
- Internal barcodes example file: internal_barcodes.csv
- Plate layout example file: plate_layout.csv
- Reference genome (size too large for upload): download from https://www.ncbi.nlm.nih.gov/genome/guide/human or scp from /mnt/storage13/ahri/human_genotyping/github/input_files/GCF_000001405.40_GRCh38.p14_genomic.fna
- gff file (size too large for upload): download from https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/ or scp from /mnt/storage13/ahri/human_genotyping/github/input_files/GCF_000001405.40_GRCh38.p14_genomic.gff
- Clinvar file (size too large for upload): download via the command below or scp from /mnt/storage13/ahri/human_genotyping/github/input_files/clinvar_GRCh38.vcf.gz
curl -s ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz > clinvar_GRCh38.vcf.gz tabix -f clinvar_GRCh38.vcf.gz