Project_tenm4_TAR-seq
Description
In this study, all individuals with SCZ were interviewed by at least two independent psychiatrists. Diagnoses were made strictly according to Diagnostic and Statistical Manual of Mental Disorders (DSM)-IV criteria, and patients with other neurological, mental or psychiatric disorders, or with history of drug use were excluded. All participants provided written informed consent. Approval was received for our study from the Ethics Committee of Human Genetic Resources of Shanghai Jiao Tong University and local hospitals. For the family-based sequencing study, a total 68 SCZ families with no less than 3 patients were selected, and a total 351 samples were collected for targeted sequencing.
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Steps to reproduce
the paired 150bp-long reads were mapped to hg19 human reference genome by Burrows-Wheeler Aligner (BWA) software. Samtools was used for sequence sorting, gene location labeling, and format transformation. Genome Analysis Toolkit (GATK) was used to identify mutation, filter and select comment to generate VCF file. All variants were annotated by ANNOVAR software (2019Oct24)., and the potential effect on the protein function were predicted by 9 software (SIFT, PolyPhen2, LRT, MutationTaster, MutationAssessor, FATHMM, PROVEAN, MetaSVM, and MetaLR). All functional mutations were one-by-one visually confirmed by IGV software (v2.8.6).