From 78945fb46fa0ead345703a37ed3e22f19bd1dc65 Mon Sep 17 00:00:00 2001
From: Elizabeth Partan <36081569+epartan@users.noreply.github.com>
Date: Fri, 7 Jun 2024 11:55:10 -0400
Subject: [PATCH] Update 13_oncoprint_creation.md

Fixed hg38 -> GRCh38.p7 in filenames
---
 lessons/13_oncoprint_creation.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/lessons/13_oncoprint_creation.md b/lessons/13_oncoprint_creation.md
index c24d977..cb7c351 100644
--- a/lessons/13_oncoprint_creation.md
+++ b/lessons/13_oncoprint_creation.md
@@ -117,13 +117,13 @@ There are four main parts to the above code:
 In order to run the code, we will need to execute:
 
 ```
-sh VCF_to_oncoprint.sh /n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_syn3_normal_syn3_tumor_hg38-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf  syn3
+sh VCF_to_oncoprint.sh /n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.vcf  syn3
 ```
 
 We can now inspect our new Oncoprinter formatted text file with:
 
 ```
-less /n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_syn3_normal_syn3_tumor_hg38-pass-filt-LCR.pedigree_header.snpeff.dbSNP.oncoprint.txt
+less /n/scratch/users/${USER:0:1}/${USER}/variant_calling/vcf_files/mutect2_syn3_normal_syn3_tumor_GRCh38.p7-pass-filt-LCR.pedigree_header.snpeff.dbSNP.oncoprint.txt
 ```
 
 Once you have done this for a given sample, you would use the `cat` command to combine all of your samples together into a single text file. However, we will just be working with a single sample in this example since we don't have access to other samples.