SNP arrays were analysed with Illumina BeadStudio, PLINK and a set of custom scripts. Exome and targeted mitochondrial sequencing reads were aligned to the reference human genome (hg19) using the Burrows-Wheeler alignment (BWA) and down-stream processing of sequence data was done with Picard v1.8, SAMtools v0.1.18 and the Genome Analysis Toolkit (GATK) version 2.2.8. Variants (SNP and Indels) were identified using GATK, following version four of the GATK Best Practice Variant Detection guide. Variants were annotated using Annovar with UCSC Known Genes models, and known polymorphisms were identified using dbSNP135, 1000 genomes and NHLBI exome project with minor allele frequencies recorded from each dataset. Subsequent analysis and identification of candidate variants was performed using an in-house workflow incorporating the annotated variant data and pedigree information.
Sandra Model Custom Set Torrent
2ff7e9595c
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