Filtering vcf(variant calling) with population gvcf(genome.vcf)

• JDK 11

git clone https://github.com/shanghungshih/GVCFiltering.git

• required 4 arguments:

  • --allele_frequency -af: Keep variants with allele frequency <= threshold (ex. 0.01, which means to keep "the variants with at least 1% of population appearance")
  • --confidence -conf: Keep variants with confidence > threshold (ex. 0.8, which means to keep "the variants with genotype information > 80% of population")
    • Calculation of confidence for each variant in population gvcf: # of samples with genotype information at the loci / # of samples
  • --population -p: Input population gvcf file (ex. population_test.gvcf)
  • --vcf -v: Input vcf file to be filtered (ex. test.vcf)

• optional argument:

  • --export_population -e: Export population gvcf file with GTF(genotype frequency), AF(allele frequency) and CONF(confidence) annotation

java -jar GVCFiltering.jar -af 0.01 -conf 0.8 -p population_test.gvcf -v test.vcf -e

• output.vcf (Note: one alternative per line!)
• output.log
• (option) output.g.vcf