LR_AmpliconSeq

minimap2 / clair3 amplicon haplotyping

Step 1: Download, and index Reference for Chr of interest (H.Sap Chr17 in this case)

mkdir Chr17Ref

wget -O ./Chr17Ref/Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz http://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz
cd ./Chr17Ref/
module load gcc/8.2.0
module load samtools/1.14
gunzip -c Homo_sapiens.GRCh38.dna.chromosome.17.fa.gz > Homo_sapiens.GRCh38.dna.chromosome.17.fa
samtools faidx Homo_sapiens.GRCh38.dna.chromosome.17.fa
cd ..

Step 2: Download Clair3 and models

#download r941-g5014 single
wget -O ./r941_prom_sup_g5014.tar.gz  http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_sup_g5014.tar.gz
gunzip r941_prom_sup_g5014.tar.gz
tar -xvf r941_prom_sup_g5014.tar

#download r941-g360+g422 single
wget -O ./r941_prom_hac_g360+g422.tar.gz  http://www.bio8.cs.hku.hk/clair3/clair3_models/r941_prom_hac_g360+g422.tar.gz
gunzip ./r941_prom_hac_g360+g422.tar.gz
tar -xvf r941_prom_hac_g360+g422.tar

# or download all models
wget -O ./clair3_models.tar.gz http://www.bio8.cs.hku.hk/clair3/clair3_models/clair3_models.tar.gz
tar -xvf ./clair3_models.tar.gz

#download clair3 .py and .sh scripts
wget -O ./clair3.py https://github.com/HKU-BAL/Clair3/blob/main/clair3.py
wget -O ./run_clair3.sh https://github.com/HKU-BAL/Clair3/blob/main/run_clair3.sh

# clone Clair3 (if preffered)
git clone https://github.com/HKU-BAL/Clair3/blob/main/clair3.py

Step3: Use LR_AmpliconSeq.sh to run Minimap2 and Clair3 for SNP dection and phasing

sbatch LR_AmpliconSeq.sh

See file ACADVL_phaseSummary.VCF for output summary, ignore SNPs that fall outside the ACADVL genomic region (17:)