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>Though that $1000 produces 100GB of data Not sure if you are referring to the raw sequence data coming from the sequencers, nowadays the standard practice is
by noname123 11y ago
>Though that $1000 produces 100GB of data
Not sure if you are referring to the raw sequence data coming from the sequencers, nowadays the standard practice is to align a specific sample's genome (e.g., an individual's genome) to the reference genome (the Human Genome Project) and store only your variations against that reference genome, stored as a BAM (binary alignment) file.
Furthermore, for most clinical cases, if you only care about the current known SNP (single nucleotide polymorphism in coding genes), you can generate a VCF file at those known SNP sites, compressing the data further. This is the way most population genetics is done by comparing the VCF files of cohorts, not doing analysis of single genomes of patients one by one.
- adenadel 11y agoYou've got a bit of misinformation in here. He's correct about the raw sequence data for a 30X whole human genome being 100GB of data. The standard practice is to align the sample to the reference, but we store alignments in the BAM file, not variations. Some of the mismatches in the alignments are due to noise in the sequencer. We run the BAM through a variant caller which outputs a VCF which contains the variants. You do not typically genotype at only known SNP sites when generating a VCF file (although you may restrict by a region). If you were only interested in certain SNP sites you would be better off running a microarray.
- jerven 11y agoOf course its a VCF file which we hope contains the variants ;( the tech is still fickle and so is some of the biology... Soon we are going to go towards variant graphs and VCFs will disappear again, slowly (IMHO).