samtools -help!

[bio_tt]

samtools packge has many tools such as samtools.pl,samtools.exe,but there are some others ,i don't know their functions,what's more, i can't get some
useful information from these tools,i hope you can tell me !

thank you ,guys

[ntremblay]

Hi,

you can view the user guide at http://samtools.sourceforge.net/samtools.shtml

Basically, Samtools is a utility that enable you to manipulate SAM/BAM alignment files.

What are you trying to do?

[bio_tt]

Hi,

you can view the user guide at http://samtools.sourceforge.net/samtools.shtml

Basically, Samtools is a utility that enable you to manipulate SAM/BAM alignment files.

What are you trying to do?

i used samtools to call snp,but in that package i found some other tools,such as blast2sam.pl ,novo2sam.pl ,sam2vcf.pl soap2sam.pl zoo2sam.pl ,and so on.
i can't find some useful information,so i don't know how to make good use of them .
thank you very much!

[Thomas Doktor]

They are merely scripts to convert other alignment formats to the SAM/BAM format. If you already have your alignments in SAM/BAM format they are of little use to you, except perhaps as code examples to learn from.

EDIT
The sam2vcf.pl script that you mention could be of use to you, if you wish to run analysis programs that support VCF but not SAM/BAM.