The detailed report contains r 2 values for all pairs of vairants above a user-specified r 2 threshold (see -tagR2Threshold). This annotator produces both a summary report and a detailed report. The r 2 values are only calculated for samples that are present in both the input VCF file and the tag VCF file. If no populations are defined, the samples in the VCF are treated as a single population. Multiple populations (potentially overlapping) may be specified and then the r 2 calculations are performed separately in each population. In the case of copy number variants, r 2 is computed with respect to diploid copy number. This annotator can process either bi-allelic variants (with GT/GQ fields) or copy-number variants (with CN/CNQ fields). VCF) specified by -tagFile, which can be the same file or a different file.įor each variant in the input variant file, a pairwise r 2 value is computed to all variants in the tag variant file within a certain genomic distance of each ![]() The TagVariants annotator compares the input variant file to a comparison file of variants (e.g. ![]() The TagVariants annotator is invoked through the SVAnnotator framework, which defines arguments common to all annotators. Annotator that evaluates tagging SNPs (or other markers) based on pairwise r 2.
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