Computational protocol: Novel rare variations of the oxytocin receptor (OXTR) gene in autism spectrum disorder individuals

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Protocol publication

[…] Raw FASTQ files from both sequencers were retrieved and aligned to the hg19 reference using Burrows–Wheeler aligner aligner tool, and subsequently converted to sort BAM files with SAMtools. SNVer, a software specifically designed to detect variants in pooled NGS data, was used for variant calling using default parameters. All variants were mapped to GRCh37 (hg19). Taking advantage of paired-end reads, variants called from only one strand were removed as false-positive findings. wAnnovar was used for variant annotation (http://wannovar2.usc.edu/). Variants not registered in either dbSNP 138 database, 1000 genome database or NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/) are regarded as novel variants. The burden analysis was performed with RAREMETAL (http://genome.sph.umich.edu/wiki/RAREMETAL). To search for putative splicing variant, we examined each variant to see whether it is located within or near-splice junctions. Furthermore, we evaluate the potential functional impacts of the nonsynonymous variants using two in silico predication tools sorting intolerant from tolerant (SIFT) and polymorphism phenotyping v2 (PolyPhen-2)., […]

Pipeline specifications

Software tools BWA, SAMtools, SNVer, wANNOVAR, RAREMETAL, SIFT, PolyPhen
Databases dbSNP
Applications WES analysis, GWAS
Organisms Homo sapiens
Chemicals Oxytocin