Variant Recalling (FreeBayes) from Whole Exome Sequencing data for 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 call and annotate SNPs and Indels on data from all three collections in a uniform manner using the latest toolchains and algorithms available.

Variant calls from this study were generated using FreeBayes, Famseq, and some custom scripts; annotation was provided by SnpEff, dbNSFP, and vcftools. Note that variants were called in batches with ~ 20 families per batch. 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 includes the genomics_sample02, genomics_sample03 structures with annotated and un-annotated VCF files for each family. Another NDAR Study (348) is available with VCF files generated using GATK (https://ndar.nih.gov/study.html?id=348), and the complete set of BAM files used for variant calling are available in NDAR Study 334 (https://ndar.nih.gov/study.html?id=334)