This pipeline was developed to identify pharmacogenetic variation in publicly avalailable archaic genomes. Contact Teddy Wroblewski (tadeusz.wroblewski@cuanschutz.edu) for more information.
- RStudio
- Python3
- pypgx
- Stargazer
- bcftools
Samples were genotyped and read depth was extracted using using pypgx - version 0.1.37
pypgx bam2vcf gatk "reference_genome" "gene" "output_name.vcf" hg19 --bam_dir "${d}/bam_Files.txt"
pypgx bam2gdf hg19 "gene" "control_gene" "output_name.gdf" --bam_list "${d}/bamFiles.txt"
Examples for CYP1A2 and CYP2A6 can be found in input/genotype/ and input/depth_of_coverage/
Genotype and read depth files were inputted into Stargazer (Lee et al. 2019) with the following command
python3 stargazer.py "genotype" -o "output_preffix" -d wgs -t "supported_gene" --vcf "input.vcf" -c "control_gene --gdf "input_rd.gdf"
Examples for CYP1A2 and CYP2A6 can be found in input/sge_output/
Stargazer
Output Processing: 2021_Archaic_PGx_SGE_Output_Analysis.R
Example output found here.
SNV Analysis
Select gene positions (start-stop gene loci + 2000bp upstream for the promoter) and filter the QUAL >= 40
bcftools view -t "chr:strt-end" "input.vcf" > "output.vcf"
bcftools view -i '%QUAL>=40' "output.vcf" > "output_filtered40.vcf"
SNVs are annotated with Annovar, CADD, SIFT, and PolyPhen2
SNV Analysis Script: 2021_Archaic_PGx_variantSNV_Analysis.R
Example output found here.
Potentially Damaging Variants
Potentially Damaging Variant Script: 2021_Archaic_PGx_potentiallyDamagingSNVs_Analysis.R
Example output found here.