A Gene-Based Recessive Diplotype Exome Scan to identify recessive and compound heterozygosity variants
Putative functional variants included in the analyses satisfied the quality control criteria as described previously. In addition, markers in the analyses were either GWAS-significant as of June 2015 and/or annotated as missense, nonsense, 3’UTR, 5’UTR or occurring within a splice site region.
In general, gametic phasing is necessary to directly determine compound heterozygous individuals at a particular gene. Several algorithms are available for inferring phased haplotypes from unphased genotype data using population-based samples, including the localized haplotype-cluster model algorithm implemented in the software Beagle. Each gene in the exome was phased separately using this method within Beagle (default method for our analysis).
FinalRelease_QC_20140311_Team1_Marshfield.10302018.annovar.hg19_multianno.csv too large (~348M) to upload to github, please send email to obtain.
2ALOF_process_sub.R: main functions in this analysis
Rscript 2ALOF_main_v5.R