PharmGKB_VCF-DataAnalysis

PharmGKB DB usage in VCF files

• This script uses R with VCF file specific preparation of VCF required
• VCF should contains lines from #CHROM as starting
• Formation of certain VCF format can be done in linux terminal or also by manual removal

Usage

Step 1:

cat input-properVCF-file.vcf | grep -v "##" > Prepared.vcf

• This can also be done by removing all lines that has ## as starting in the VCF file

Step 2:

Rscript PharmGKB_VCF_analysis.R Prepared.vcf output-file-name

• The Rscript will take the input VCF file and generate .csv file as output
• The CSV output file has same prefix as the input VCF file
• output-file-name can be given by user to make .csv file output

Conditions

• Make sure VCF file is annotated properly for getting ID. The complete script depends on ID column data.
• Make sure VCF format is proper with starting line is from #CHROM line as usually present.
• Make sure to provide input file name properly with extension and provide output file name alone

Columns available in .csv file

• The same model output file is also present for reference.

Clinical.Annotation.ID	Gene	Level.of.Evidence	Score	Phenotype.Category	Drug	Phenotype	CHROM	POS	QUAL	INFO	REF	ALT	Annotation.Text

Note

• PharmGKB is downloaded and used for this analysis on August 2023.
• Feel free to update the script or DB for your usage