I know that HaplotypeCaller is designed to call germline variants which is different from the reference genome. Knowing the fact that somatic mutations are also different from the reference genome HaplotypeCaller picks these variations into account. Hence, the variants called by HaplotypeCaller contains both Germline and Somatic Variants. Is this right?
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svp
1 answer
HaploypeCaller is optimized for a ploidy of 2, and the ploidy can be changed on the command line. That ploidy doesn't work for somatic variants, so the assumptions of variant calling are different for germline vs somatic. It is possible that you will find some somatic variants in your haplotypecaller results (probably with low quality and a low allelic frequency), but it is not recommended to use haplotypecaller with the intention to identify somatic variants.
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