IV.3_SNP_mv20.vcf

De novo mutations observed in individual IV.3. Sequenced reads were aligned to the hg19 reference human genome downloaded from UCSC and aligned using Burrows–Wheeler alignment (BWA-MEM). <em>De novo</em> mutations were called using standard GATK4 best practices pipeline. All samples were jointly called, but only high-confidence mendelian violation sites with minimum GQ=20 for each trio member were selected. Subsequently, additional filters were applied: i) coverage of each trio member ≥10; ii) absence of reads confirming alternative allele in parents; iii) number of reads confirming reference and alternative allele in proband ≥5; iv) allele frequency of the alternative allele in the proband ≥0.3. Additionally, clustered mutations (distance between mutations ≤1000bp) were filtered out, as potential false positives. Mutations present in any other family member were also excluded. To eliminate false positive mutations coming from the sequencing of proband fibroblasts, we used other fibroblasts from the same individual (used in MA experiments) as additional confirmation of mutation presence.