文章目录
By default, pVACseq will evaluate all somatic variants in the input VCF in isolation. As a result, if a somatic variant of interest has other somatic or germline variants in proximity, the calculated wildtype and mutant protein sequences might be incorrect because the amino acid changes of those proximal variants were not taken into account.
To solve this problem, we added a new option to pVACseq in the pvactools release 1.1. This option, --phased-proximal-variants-vcf, can be used to provide the path to a phased VCF of proximal variants in addition to the normal input VCF. This VCF is then used to incorporate amino acid changes of nearby variants that are in-phase to a somatic variant of interest. This results in corrected mutant and wildtype protein sequences that account for proximal variants.
At this time, this option only handles missense proximal variants but we are working on a more comprehensive approach to this problem.
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