We have WGS samples with an average depth of 10x and we would like to get millions of loci genotyped accurately, is this enough? What should I expect? When I run haplotypecaller I only get about ~500,000 sites in the VCF file.
We have WGS samples with an average depth of 10x and we would like to get millions of loci genotyped accurately, is this enough? What should I expect? When I run haplotypecaller I only get about ~500,000 sites in the VCF file.
The typical coverage for human WGS samples nowadays is 30X to 50X. You can then expect to detect 4-5M variants.
There have been done numerous studies on the effect of sequencing coverage on variant detection, for example this one. They typically downsample the data for their assessment. You would expect to get 0.5 sensitivity for variant detection at 10X sequencing.
I have personally not seen any WGS samples sequenced with 10X, yet I would expect more variants than 0.5M. I suspect there are problems in either your data analysis or the data itself.
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I agree with mfasold, you may do not see clearer difference of variants in 10x. When it comes to analysis, moreover if you apply with mapping, maybe the difficulties are going to be started.