Genomics

Data pre-processing is the obligatory first phase that must precede all variant discovery. It involves pre-processing the raw sequence data (provided in FASTQ or uBAM format) to produce analysis-ready BAM files. This involves alignment to a reference genome as well as some data cleanup operations to correct for technical biases and make the data suitable for analysis. This is avaialble as part of the Genome Analysis ToolKit’s (GATK) best practices and workflows.

Identify germline short variants (SNPs and Indels) in one or more individuals to produce a joint callset in VCF format, available as part of Genome Analysis ToolKit’s (GATK) best practices and workflows.