We called de novo variants using a combination of PLINK/SEQ (Fromer et al., 2014) and in-house scripts (see https://bitbucket.org/willseylab/tourette_phase1 for example commands). Empirically validated filters identified high confidence de novo SNVs and indels (see Sanders et al., 2012). Briefly, we called a de novo variant if: The child was heterozygous for a variant with alternate allele frequency (AB) between 0.3 and 0.7 in the child and ≤ 0.05 in the parents (i.e., not present)Minimum sequencing depth ≥ 20 in all family members at the variant positionAllelic depth for the alternate allele (AD) ≥ 8Observed allele frequency in the respective cohort ≤ 0.001Minimum map quality ≥ 30Minimum phred-scaled genotype likelihood ≥ 20
