From 509b933454125ef4a6b28af8f4b5fb14039d1771 Mon Sep 17 00:00:00 2001
From: Susanna Kiwala <susanna.kiwala@wustl.edu>
Date: Mon, 23 Sep 2024 12:28:07 -0500
Subject: [PATCH] Update readcounts.rst

---
 docs/pvacseq/input_file_prep/readcounts.rst | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/pvacseq/input_file_prep/readcounts.rst b/docs/pvacseq/input_file_prep/readcounts.rst
index ffd281a2a..2cd2d57d1 100644
--- a/docs/pvacseq/input_file_prep/readcounts.rst
+++ b/docs/pvacseq/input_file_prep/readcounts.rst
@@ -134,7 +134,7 @@ from a VCF and run bam-readcount. Information on that Docker container can be fo
 .. code-block:: none
 
    /usr/bin/python /usr/bin/bam_readcount_helper.py \
-   <decomposed_vcf> <sample_name> <reference_fasta> <bam_file> <output_dir>
+   <decomposed_vcf> <sample_name> <reference_fasta> <bam_file> NOPREFIX <output_dir>
 
 This will write two bam-readcount files to the ``<output_dir>``:
 ``<sample_name>_bam_readcount_snv.tsv`` and