update script for merging cnv files

d3b-center · Jul 17, 2023 · aea6685 · aea6685
1 parent 3bde20f
commit aea6685
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/analyses/copy_number_consensus_call/merge_cnv_file.R b/analyses/copy_number_consensus_call/merge_cnv_file.R
@@ -4,11 +4,11 @@ library(tidyverse)
 root_dir <- rprojroot::find_root(rprojroot::has_dir(".git"))
 cnv_gatk_dir <- file.path(root_dir, "analyses", "copy_number_consensus_call", "results")
 cnv_manta_dir <- file.path(root_dir, "analyses", "copy_number_consensus_call_manta", "results")
-output_file <- file.path(cnv_gatk_dir, "cnv-consensus_full.seg.gz")
+output_file <- file.path(cnv_gatk_dir, "cnv-consensus.seg.gz")
 
 # read cnv files
-cnv_gatk <- readr::read_tsv(file.path(cnv_gatk_dir, "cnv-consensus.seg.gz"))
-cnv_manta <- readr::read_tsv(file.path(cnv_manta_dir, "cnv-consensus.seg.gz"))
+cnv_gatk <- readr::read_tsv(file.path(cnv_gatk_dir, "cnv-consensus-freec-ckit-gatk.seg.gz"))
+cnv_manta <- readr::read_tsv(file.path(cnv_manta_dir, "cnv-consensus-freec-ckit-manta.seg.gz"))
 
 # merge two files together
 merged <- rbind(cnv_gatk, cnv_manta) %>%