How to use SAMtools?

[cgjkjk]

Hi all
I am a newbie for SAMtools, trying to find SNPs. However, SAMtools (version 0.1.18)didn't return the right result.

My command: samtools pileup -f hs_ref_GRCh37.p5_chrX.fa sub1.bam chrX > hs.txt. The result contains the information of all bases, such as:
chrX 2 N 1 ^!t I
chrX 3 N 1 a I
chrX 4 N 1 a I
chrX 5 N 1 c I
chrX 6 N 2 c^!c II
chrX 7 N 2 cc II
chrX 8 N 2 tt II
......

When I try 'mpileup' command, system warns:[main] unrecognized command 'mpileup'.

Please, I need your help.
Thanks

[Heisman]

Pretty sure pileup is gone so shouldn't work. Here are commands that work for me. Not sure if this is ideal, though.

/samtools-0.1.18/samtools mpileup -ugf [Reference_Sequence] [Aligned_File] | /samtools-0.1.18/bcftools/bcftools view -bvcg -> [Intermediate_File] &

/samtools-0.1.18/bcftools/bcftools view [Intermediate_File] | /samtools-0.1.18/bcftools/vcfutils.pl varFilter -D99999 > [Called_Variants] &

[cgjkjk]

I got it.
Thanks Heisman