Computational protocol: Rate of de novo mutations, father’s age, and disease risk

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Protocol publication

[…] Whole genome sequence data for this study were generated using the Illumina GAllx and HiSeq2000 instruments. The sequencing reads were aligned to the hg18 reference genome with BWA and duplicates were marked with Picard [http://picard.sourceforge.net/]. Quality score recalibration, indel realignment and SNP/Indel discovery was then performed on each sample separately, using GATK 1.2 (Ref. ). Likelihoods presented are based on the normalized Phred-scaled likelihoods that are calculated by the GATK variant calling. Statistical analysis was performed in part using the R statistical package. Estimates and confidence intervals for the fraction of variance explained after accounting for Poisson variation were calculated using Monte Carlo simulations (). Variants were annotated using SNP effect predictor (snpEff2.0.5, database hg36.5) and Genome Analysis Toolkit 1.4-9-g1f1233b with only the highest-impact effect (Cingolani, P. “snpEff:Variant effect prediction”, http://snpeff.sourceforge.net, 2012). More details in . […]

Pipeline specifications

Software tools BWA, Picard, GATK, SnpEff
Application WGS analysis
Organisms Homo sapiens