Generate diagnostic plots for SNV & InDel variant calling QC checks

Single command to generate a comprehensive set of diagnostic plots that assist in performing QC checks of SNVs & InDels called from MGP1000 using union consensus. Can be used as both a first pass of unfiltered variants to see consensus skew as well as used after filtering to show changes in calling metrics.

Usage

get_qc_diagnostics_snvindel(
  path_to_snv_dir = NULL,
  path_to_indel_dir = NULL,
  snv_indel_obj = NULL,
  plot_sample_names = T,
  include_caveman = F
)

Arguments

path_to_snv_dir

Path to directory of MGP1000 union consensus SNVs

path_to_indel_dir

Path to directory of MGP1000 union consensus InDels

snv_indel_obj

Data.table object with merged SNVs & InDels, used in place of paths to directories

plot_sample_names

Output plots to include sample names on y-axis, default: TRUE

include_caveman

Add caveman to consensus list if used in SNV variant calling, default: FALSE

Value

Patchwork 'quilt'-like plot of ggplots