In BrentLab/brentlabRnaSeqTools: Management/QC for brentlab RNAseq data

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = TRUE,
  include = TRUE,
  eval = FALSE
)

Using the Variant Explorer

These are preliminary notes on using the Variant Explorer object

library(brentlabRnaSeqTools)
#devtools::load_all("../R")

create a sample metadata frame

gff = rtracklayer::import("~/ref/KN99/current_htcf_genome/KN99_stranded_annotations_fungidb_augment.gff")

snpeff_files = Sys.glob("/mnt/scratch/variant_calling_pipeline/genotype_check/run_6023/variant_annote/bwamem2/snpeff/*txt")
names(snpeff_files) = ifelse(str_extract(snpeff_files, "tiddit|dusted") == 'tiddit', 'tiddit', 'freebayes')
snpeff_files  = snpeff_files[names(snpeff_files)=='freebayes']

bam_list = Sys.glob("/mnt/scratch/share_genotype_results/run_6023_results/alignment/*bam")
names(bam_list) = str_extract(bam_list, "sample_\\d+")

sample_meta = tibble(sample_id = str_extract(snpeff_files, "sample_\\d+"),
                     snpeff = snpeff_files,
                     variant_caller = names(snpeff_files)) %>%
  left_join(tibble(sample_id = names(bam_list), bam = bam_list))

Instantiate a VarianetExplorer

ve = create_variant_explorer(sample_meta,
                             gff,
                             igv_genome = "~/ref/KN99/current_htcf_genome/kn99_stranded.genome",
                             BSgenome.CneoformansVarGrubiiKN99.NCBI.ASM221672v1)

Get an overview of the variants present in your samples

summary(ve)
#ve = rank_results(ve)

look at the

view_variants(ve@variants)

visualize(ve,'CKF44_01599', "sample_5", 'pileup')

igv_script(ve, "CKF44_02980")

BrentLab/brentlabRnaSeqTools documentation built on Aug. 20, 2023, 9:22 a.m.