Whole Exome Sequencing Analysis Pipeline

Libraries were prepared with the SureSelect Human All exon V2 kit (Agilent Technologies Inc, USA). Paired-end sequencing was performed on the Illumina Genome Analyzer II platform (Illumina Inc, USA). The sequence reads were aligned to the Human Reference Genome Build hg19 using the BWA software^{18 (link)}, followed by GATK base quality score recalibration, duplicate marking and local realignment. SNPs and indels were simultaneously called in all samples using the GATK HaplotypeCaller algorithm, applying hard-filtering parameters according to GATK best practices recommendations¹⁹ . Variants were annotated and prioritized using ediva, our in-house pipeline (www.ediva.crg.eu), which provides information on minor allele frequencies from various databases, including the Exome Aggregation Consortium, and Exome Variant Server-NHBLI, variant functional effect prediction scores by SIFT, Polyphen2, MutationAssessor and CADD, and variant conservation scores PhyloP and Gerp++. Fastq files can be accessed through EGA (EGAS00001003510).