Pipeline-description.md

@@ -184,13 +184,13 @@ This command is used to view and convert SAM, BAM and CRAM files. It can be used
 **Command line example**:
 
 ```bash
-samtools view -F 0x100 --output-fmt BAM -o <out.bam> <in.sam>
+samtools view -F 0x100 -b -o <out.bam> <in.sam>
 ```
 
 **Arguments**:
 
 - _-F \<flag\>_: only include reads with none of the flags present
-- _--output-fmt \<SAM/BAM/CRAM\>_: output in the format SAM, BAM or CRAM
+- _-b_: output in the format BAM
 - _-o \<out.bam\>_: output file name
 
 #### Samtools faidx