VariantReporterSpark

Scalable application for prioritising clinically relevant variants from WGS/WES/Panel studies built using Apache Spark.

This software will extract annotated variants to text file that fall into these categories:

• Dominant inheritance
• Recessive inheritance
• Compound Heterozygous inheritance
• De Novo (trio only)
• Uniparental disomy (trio only)

Usage

Perform variant calling, filtering and annotation using the GermlineEnrichment pipeline.

Run variant prioritise workflow

/share/apps/jre-distros/jre1.8.0_131/bin/java \
-Djava.io.tmpdir=/state/partition1/tmpdir \
-Xmx48g \
-jar /data/diagnostics/apps/VariantReporterSpark/VariantReporterSpark-1.3.2/VariantReporterSpark.jar \
-V calls.vcf \
-P pedigree.ped \
-T <threads> \
-N

Theory of operation

Variants are passed through a series of filters as shown in the flowchart and described below.

Non Informative Site Filter

Identifies variant sites for downstream analysis

• Pass all context filters (Quality, QD, FS, MQ, MQRankSum, ReadPosRankSum, InbreedingCoeff)
• Has functional annotation
• Non reference in one or more samples
• Less than 1% population allele frequency (Gnomad) for one or more alternative alleles

Non Variant By Sample Filter

Identifies genotypes for downstream analysis

• Must pass genotype filters (DP >10, GQ > 20)
• Cannot be homozygous for the reference allele
• Cannot be no call (insufficient data to call genotype)

Dominant Filter

• Autosomal
  • Heterozygous
  • Cohort allele count < 4
  • gnomAD (Exome) allele frequency < 0.1%
  • gnomAD (Genome) allele frequency < 0.75%
• X-Female
  • As autosomal
• X/Y-Male
  • Homozygous (hemizygous)
  • Cohort allele count < 6
  • gnomAD (Exome) allele frequency < 0.1%
  • gnomAD (Genome) allele frequency < 0.75%

Homozygous Filter

• Autosomal
  • Homozygous for alternative allele
  • Cohort allele count < 4
  • gnomAD (Exome) allele frequency < 1%
  • gnomAD (Genome) allele frequency < 1%
• X-Female
  • Homozygous for alternative allele
  • Cohort allele count < 8
  • gnomAD (Exome) allele frequency < 1%
  • gnomAD (Genome) allele frequency < 1%

Compound Heterozygous Filter

• Autosomal or X-Female
  • Heterozygous
  • gnomAD (Exome) allele frequency < 1%
  • gnomAD (Genome) allele frequency < 1%
  • Two or more variants per gene

De Novo Filter

• Any chromosome
  • Both parents are homozygous reference
  • Cohort allele count < 4
  • gnomAD (Exome) allele frequency < 0.1%
  • gnomAD (Genome) allele frequency < 0.75%

Uniparental Isodisomy Filter

• Autosomal
  • Homozygous for alternative allele
  • Mother is heterozygous and father is homozygous reference OR mother is homozygous reference and father is heterozygous
  • gnomAD (Exome) allele frequency < 1%
  • gnomAD (Genome) allele frequency < 1%
• X-Female
  • Homozygous for alternative allele
  • Mother is heterozygous and father is homozygous reference OR mother is homozygous reference and father is homozygous (hemizygous) alternative
  • gnomAD (Exome) allele frequency < 1%
  • gnomAD (Genome) allele frequency < 1%

Functional Consequence Filter

Variant has consequence on one or more transcripts

• frameshift_variant
• incomplete_terminal_codon_variant
• inframe_deletion
• inframe_insertion
• initiator_codon_variant
• missense_variant
• splice_acceptor_variant
• splice_donor_variant
• splice_region_variant
• stop_gained
• stop_lost
• synonymous_variant
• transcript_ablation
• transcript_amplification