Computational protocol: Exome sequencing improves genetic diagnosis of structural fetal abnormalities revealed by ultrasound

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Protocol publication

[…] For detailed methodology see Supplementary Material, Appendix. In brief, DNA samples were exome sequenced using a SureSelect All Exon capture kit (Agilent, Wokingham, UK) followed by paired-end sequencing (75 bp reads) on the HiSeq platform (Illumina, Saffron Walden, UK). Reads were mapped to the reference human genome GRCh37_hs37d5. Duplicate reads were removed and reads were realigned around potential indels. We called variants using SAMtools, GATK and Dindel. The EGA ID for the exome sequencing data is EGAS00001000167 (https://www.ebi.ac.uk/ega/).To identify de novo mutations, we used De Novo Gear pipeline version 0.6.2 (). We considered rare, high-quality variants in protein-coding exons. To identify inherited recessive and X-linked SNVs and indels, we first merged the VCFs from the three variant callers for each individual, and then we identified genes harboring rare, high-quality, functional variants (predicted protein consequences were essential splice site, stop gained, frameshift coding, non-synonymous, stop lost) under the different plausible modes of inheritance (recessive or X-linked). To discover CNVs from the exome data, we used CoNVex (ftp://ftp.sanger.ac.uk/pub/users/pv1/CoNVex/). We filtered out CNVs that were low confidence, overlapped common CNVs, did not overlap protein-coding genes or did not fit with the expected mode of inheritance (de novo, inherited recessive or X-linked). […]

Pipeline specifications

Software tools SAMtools, GATK, Dindel
Application WES analysis
Organisms Cucumber necrosis virus
Diseases Genetic Diseases, Inborn