Table 2 Cohort information and technical features WES
From: Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP
DDD (n = 7357)a | CRC (n = 517) | GS (n = 315) | |
|---|---|---|---|
Capture kit | Agilent Human All-Exon V3 or V5 Plus with custom ELID C0338371 | Illumina TruSeq Exome Enrichment kit | Illumina TruSeq Exome Enrichment kit |
Sequencing platform | Illlumina HiSeq | Illumina HiSeq 2000 and 2500 | Illumina HiSeq 2000 and 2500 |
Alignment | bwa (0.5.9) | bwa (0.5.9) | bwa (0.5.9) |
Variant calling | GATK (3.1.1) | GATK (3.4) | GATK (3.4) |
Indel realignment, BQSR | Indel realignment, BQSR | Indel realignment, BQSR | |
HaplotypeCaller (run in multisample calling mode using the complete dataset) | HaplotypeCaller (per sample) | HaplotypeCaller (per sample) | |
GenotypeGVCFs (joint genotyping across all samples on TruSeq regions + 50 bp padding) | GenotypeGVCFs (joint genotyping across all samples on TruSeq regions + 50 bp padding) | ||
Relatedness | After excluding poor quality samples, selected randomly one affected proband per family (using the PED file) | Unrelated | First-degree relatives excluded (based on computed relationship coefficients) |
Male:female ratio | 1.36 | 1.11 | 0.73 |
Median age | 7.9 years | 63 years | 52 years |
