In hubentu/VarReviewer: Variant Reviewer

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

suppressPackageStartupMessages(
    library(VarReviewer)
)
library(BSgenome.Hsapiens.1000genomes.hs37d5)

View BAM for a variant

bam <- system.file("extdata", "test.bam", package="VarReviewer")
vcf <- system.file("extdata", "test.vcf", package="VarReviewer")
v1 <- readVcf(vcf)

viewAligns(rowRanges(v1), bam)

{width=600px}

Re-align BAM and VCF to SE

Re-align counts

To realign reads locally to reference and alternative sequences for given variant.

rse <- reAlign(rowRanges(v1), bam)
rse
assays(rse)$ADP[1,1][[1]]

View alignments

A "YC" tag will be added to the outputs to label reads with different alignments using different colors.

aln <- assays(rse)$Align[1,1][[1]]
viewAligns(aligns = aln, bamParam=list(tag="YC"))

{width=600px}

hubentu/VarReviewer documentation built on June 7, 2019, 12:48 a.m.