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Genotype Level Columns

  • Sample Name: CHGVID from Sequence (LIMS)
  • Sample Type: genome_as_fake_exome, exome or custom_capture
  • Sample Phenotype: case or ctrl
  • GT: hom re, het or hom
  • DP: variant caller DP
  • DP Bin: calculated from BAM, values: NA (0-9), 10 (10-19), 20 (20-29), 30 (30-49), 50 (50-199), 200 (200+)
  • AD REF: quality stat from GATK
  • AD ALT: quality stat from GATK
  • Percent Alt Read: percentage of all the reads at the site that support the alternative allele
  • Percent Alt Read Binomial P: binomial Exact one-tail p-value permitted for the alt:ref ratio discrepancy from expected 0.5
  • GQ: quality stat from GATK
  • VQSLOD
  • SOR: quality stat from GATK
  • FS: quality stat from GATK
  • MQ: quality stat from GATK
  • QD: quality stat from GATK
  • Qual: quality stat from GATK
  • Read Pos Rank Sum: quality stat from GATK
  • MQ Rank Sum: quality stat from GATK
  • FILTER: Filter is based on GATK's VQSR method. We defined four tranches: PASS, LIKELY, INTERMEDIATE, FAIL. Pass has the lowest sensitivity for detecting true variants, but is very specific. Each subsequent tranche introduces additional true positive calls along with a growing number of false positive calls.