From 092c08586ecb12ebb5886c2ea68e5cb45d2c9716 Mon Sep 17 00:00:00 2001
From: Natasha Pavlovikj <npavlovikj2@unl.edu>
Date: Tue, 1 Dec 2020 14:35:33 -0600
Subject: [PATCH] Add output flag

---
 .../samtools/running_samtools_commands.md                     | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md b/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md
index 0a9787f7..ac5c097a 100644
--- a/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md
+++ b/content/applications/app_specific/bioinformatics_tools/data_manipulation_tools/samtools/running_samtools_commands.md
@@ -39,7 +39,7 @@ The most intensive SAMtools commands (**samtools view**, **samtools sort**) are
 
 Sorting BAM files is recommended for further analysis of these files. The BAM file is sorted based on its position in the reference, as determined by its alignment. An example of using `4 CPUs` to sort the input file `input_alignments.bam` by the read name follows:
 {{< highlight bash >}}
-$ samtools sort -n -@ 4 input_alignments.bam output_alignments_sorted
+$ samtools sort -n -@ 4 input_alignments.bam -o output_alignments_sorted
 {{< /highlight >}}
 
 
@@ -79,7 +79,7 @@ $ samtools faidx input_reference.fasta
 
 The **samtools mpileup** command generates file in `bcf` or `pileup` format for one or multiple BAM files. For each genomic coordinate, the overlapping read bases and indels at that position in the input BAM file are printed.
 {{< highlight bash >}}
-$ samtools mpileup input_alignments_sorted.bam > output_alignments.bcf
+$ samtools mpileup input_alignments_sorted.bam -o output_alignments.bcf
 {{< /highlight >}}
 
 
-- 
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