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GVCFiltering

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

Prerequisite

  • JDK 11

Installation

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

Quick start

Filtering with Allele Frequency(AF) and Confidence(Conf)

  • 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

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

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Filtering vcf with population gvcf

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