Variant Annotation and Filtration with External Databases enhance the analysis of genetic variations by leveraging external databases to provide additional information about variants. This process aids in filtering and prioritizing variants based on various annotations.

Gene

Gene feature Annotation & Filtration

Gene feature annotation is used to identify which gene or transcript is affected by a variant and what functional role it has on known genes. We now support two gene definition systems: RefSeq genes (refgene) and GENCODE genes (gencode).

Options

The tutorial command is:

java -Xmx8g -jar ../kggsum.jar \
   annot \
   --sum-file ./scz_gwas_eur_chr1.tsv.gz \
              cp12Cols=CHR,BP,A1,A2 \
              pbsCols=P,OR,SE \
              betaType=2 \
              prevalence=0.01 \
   --ref-gty-file ./1kg_hg19_eur_chr1.vcf.gz \
              refG=hg19 \
   --gene-model-database refgene \
   --gene-model-database gencode \
   --threads 18 \
   --output ./ta1

KGGA has 18 number codes for the gene features after annotation.

Output

The gene feature annotation results are saved in OutputVariants2TSVTask/variants.hg38.tsv.gz. There are two relevant columns in the file:

Function

Functional score annotation at variants

In KGGSum, the GWAS variants can also be annotated with multiple genomic features. Three databases are available: gnomAD for allele frequency annotation, CADD for variant function annotation, and ClinVar for disease linkage annotation. Note that the annotation datasets should be downloaded from an independent resource domain of KGGA.

Options

The tutorial command is:

java -Xmx8g -jar ../kggsum.jar \
   annot \
   --sum-file ./scz_gwas_eur_chr1.tsv.gz \
              cp12Cols=CHR,BP,A1,A2 \
              pbsCols=P,OR,SE \
              betaType=2 \
              prevalence=0.01 \
   --ref-gty-file ./1kg_hg19_eur_chr1.vcf.gz \
              refG=hg19 \
   --variant-annotation-database cadd \
              field=Epigenetics::EncodeDNase-max,Epigenetics::EncodeDNase-sum,ProteinFunction::CADD_PHRED \
   --threads 18 \
   --output ./ta2

Additional epigenetic resources from third-party databases

To facilitate the convenient use of more resources, KGGSum provides an interactive approach that allows users to specify customized third-party resources for annotation. For example, by setting the file name documented in EpiMap, KGGSum can directly download epigenetic marker resources from the EpiGenome public domain, specifically from the EpiMap Repository.

Frequency

Allele Frequency Annotation & Filtration

Allele frequency annotation allows users to incorporate population-level allele frequency information into the analysis of genetic variants. Click to view the provided allele frequency annotation databases.

Options

The tutorial command is:

java -Xmx4g -jar ../kggsum.jar \
   annot \
   --sum-file ./scz_gwas_eur_chr1.tsv.gz \
              cp12Cols=CHR,BP,A1,A2 \
              pbsCols=P,OR,SE \
              betaType=2 \
              prevalence=0.01 \       
   --ref-gty-file ./1kg_hg19_eur_chr1.vcf.gz \
              refG=hg19 \
   --freq-database gnomad \
              field=gnomAD_joint::ALL,gnomAD_joint::NFE \
   --threads 18 \
   --output ./ta3

Once the reference databases for allele frequency annotation have been properly configured, you can effectively filter variants by examining their allele frequencies within the reference population.