case variants to the (typically unfiltered)
control variants and returns
case, with the additional
control.total.depth, corresponding to
annotateWithControlDepth(case, control, control.cov)
The variants of interest, as a
The control variants, typically unfiltered, as a
The control coverage, as an
case variant is not found in
control, a count of
0 is assigned to
control.alt.depth, under the assumption
control object is not filtered, i.e., it contains the
case, plus two new metadata columns,
callSampleSpecificVariants, which uses this function.
1 2 3 4 5 6 7 8
bams <- LungCancerLines::LungCancerBamFiles() tally.param <- TallyVariantsParam(gmapR::TP53Genome(), high_base_quality = 23L, which = gmapR::TP53Which()) case <- callVariants(bams$H1993, tally.param) control <- tallyVariants(bams$H2073, tally.param) control.cov <- coverage(bams$H2073) annotateWithControlDepth(case, control, control.cov)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.