Hi,
We are sequencing both exome and whole genome at 30x coverage. I used exome coordinate bed file to intersect it with the Whole genome bam file in order to extract the exome from the whole genome. To my surprise, I got only 8 million reads of exome from the WG whereas our exome sequencing produces around 40-45 million reads. However the coding variants from this are almost same as the exome (20-22 thousands). May I know why is it like this?
We are sequencing both exome and whole genome at 30x coverage. I used exome coordinate bed file to intersect it with the Whole genome bam file in order to extract the exome from the whole genome. To my surprise, I got only 8 million reads of exome from the WG whereas our exome sequencing produces around 40-45 million reads. However the coding variants from this are almost same as the exome (20-22 thousands). May I know why is it like this?
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