Pipeline-description.md

@@ -151,13 +151,14 @@ This command is used to view and convert SAM, BAM and CRAM files. It can be used
 **Command line example**:
 
 ```bash
-samtools view -F 256 --output-fmt BAM <in.sam>
+samtools view -F 256 --bam --output <out.bam> <in.sam>
 ```
 
 **Arguments**:
 
 - _-F \<flag\>_: only include reads with none of the flags present
-- _--output-fmt \<SAM/BAM/CRAM\>_: convert file to SAM, BAM or CRAM format
+- _--bam_: output in the BAM format
+- _--output \<out.bam\>_: output file name
 
 #### Samtools faidx