de novo Mutations

This step uses granite novoCaller to call de novo mutations for a trio (proband, mother and father). The algorithm handles both SNVs and INDELs and uses allele counts information for the trio and a panel of unrelated individuals to assigning a posterior probability to each variant call. The output vcf file is checked for integrity to ensure the format is correct and the file is not truncated. See granite repository and documentation for more information.

  • CWL: workflow_granite-novoCaller-rck_plus_vcf-integrity-check.cwl

Requirements

The input is a vcf file with genotype information for both the proband and the parents. The software also requires two rck.tar files, one for the trio and one for the panel of unrelated individuals. The rck.tar files are archives of rck files created from the corresponding bam files to record allele-specific and strand-specific read counts information.

Output

The step creates an output vcf file that contains the same variants as the input file (no line is removed), but with additional information added by the caller (novoPP and RSTR).

An example:

chr1  1041200 .    C    T    573.12 .    AC=2;AF=0.333;AN=6;BaseQRankSum=0.408;DP=76;ExcessHet=3.01;FS=3.873;MLEAC=2;MLEAF=0.333;MQ=60.00;MQRankSum=0.00;QD=13.65;ReadPosRankSum=0.155;SOR=1.877;gnomADgenome=7.00849e-06;SpliceAI=0.11;VEP=ENSG00000188157|ENST00000379370|Transcript|missense_variant|AGRN|protein_coding;novoPP=0.0  GT:AD:DP:GQ:PL:RSTR   0/1:9,4:13:99:100,0,248:6,5,4,2 0/0:34,0:34:96:0,96,1440:23,0,11,0   0/1:12,17:29:99:484,0,309:12,17,2,4   ./.:.:.:.:.:29,0,20,0  ./.:.:.:.:.:19,0,16,0  ./.:.:.:.:.:16,1,22,0  ./.:.:.:.:.:21,0,18,0  ./.:.:.:.:.:28,0,22,0  ./.:.:.:.:.:20,0,24,0  ./.:.:.:.:.:21,0,26,0  ./.:.:.:.:.:11,0,11,0  ./.:.:.:.:.:15,0,13,0  ./.:.:.:.:.:29,0,22,0

novoPP

The novoPP tag is added to the INFO field of each variants and stores the posterior probability calculated for the variant (0 < novoPP <= 1). A high novoPP value suggests that the variant is likely to be a de novo mutation in the proband.

Notes:

  • If the parents have 3 or more alternate reads, novoCaller assigns a novoPP=0 to highlight that the variant is highly unlikely to be a de novo mutation
  • The model used by novoCaller does not fit unbalanced chromosomes, currently we do not report novoPP for chrX, Y, or M, except when novoPP=0

RSTR

The RSTR value is added to each sample genotype and stores the corresponding reads counts by strand at position for reference and alternate alleles used by the caller as Rf,Af,Rr,Ar (R: ref, A: alt, f: forward, r: reverse).

References

granite.