Merge branch 'fix_samtools_command' into 'master'

Add output flag for samtools

See merge request !247

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 >}}