A joint variant call-set for all Simons Simplex Collection whole-genome sequences is now available

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The Simons Foundation Autism Research Initiative (SFARI) is pleased to announce the availability of a uniform call-set of joint variant calls, including single-nucleotide variants (SNVs) and indels, for 9,209 samples with whole-genome sequence (WGS) data from the Simons Simplex Collection (SSC).

The relevant files have been added to the joint genotyping (JG) folders of the SSC WGS endpoints at the Simons Foundation server (data transferred via globus.org) and Amazon Web Services (cloud-based access to data).

The call-set is automatically available to all investigators who have already received approval to access SSC WGS data sets. Those who have not yet been approved can apply via SFARI Base (Note: please select the “SSC Whole-genome 2” data set during the request process). Questions about access should be directed to [email protected].

This uniform call-set was generated by the New York Genome Center using the pipeline developed by the Centers for Common Disease Genomics, which is a multisite National Institutes of Health-funded effort for genetic risk variant discovery in neuropsychiatric, cardiovascular and immune-mediated diseases. The standardized variant calling pipeline employs best practices and allows large data sets to be compared across cohorts and across sequencing centers.

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