Complete Realignment of Whole Exome Sequencing data from 2415 families in SSC Collection

Whole Exome Sequencing has been completed for ~ 2500 families from the Simons Simplex Collection. Sequencing was performed at three individual sequencing centers with original data submitted to NDAR Collections 1878, 1895, and 1936; subsets of these data have been analyzed by various methods and published. This study represents an effort to realign sequencing data from all three collection sin a uniform manner using the latest toolchains and algorithms available, which can be used as a resource for the entire ASD Community. Original sequence data has been realigned to a single reference genome (1000 Genomes / GRCh37) using BWA, Picardtools, Samtools, and some custom python scripts. QC summary data were generated as part of the realignment process using the aforementioned tools in addition to QPLOT and some custom scripts. Complete methods, including source code for pipeline and custom scripts can be found at: https://github.com/nkrumm/asd-jre-public. The data package for this study represents the genomics_subject02, genomics_sample03, and omics_qa01 data structures which include realigned BAM files and QC files (i.e., QPLOT output and BAM header files). Variant calling an annotation for these data are provided in NDAR Studies 348 (https://ndar.nih.gov/study.html?id=348) and 349 (https://ndar.nih.gov/study.html?id=349).