The Complete Genomics Tool Repository contains scripts and automated workflows created by Complete Genomics experts to help you analyze Complete Genomics data. Please note that, unlike Complete Genomics official CGA™ Tools package, the scripts and programs available in the Complete Genomics Tool Repository are not formal product offerings, and as such are not fully supported by Complete Genomics.
Format Conversion
• masterVar format to VCF v4.1 format file converter rev1
• Create PLINK files from the output of the ‘testvariants’ tool
• Convert CNV Details to wig and generate a BED file
• Generate gene listvariants from gene file
• var File SNPs to PLINK converter
Genome Analysis and Comparison
• Generate distributions of metrics from summary files
• Find MIEs within a trio with stats