Commit d86ffe67 authored by Adam Caprez's avatar Adam Caprez
Browse files

Merge branch 'fix_samtools_command' into 'master'

Add output flag for samtools

See merge request !247
parents c994dd16 092c0858
......@@ -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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