SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Augustus command line help needed gomahony Bioinformatics 2 05-07-2012 11:02 AM
Want to use extract_genomic_dna in command line louis7781x Bioinformatics 2 12-04-2011 05:51 AM
Newbler runMapping via command line hlwright 454 Pyrosequencing 2 04-04-2011 11:27 PM
galaxy command line error gfmgfm Bioinformatics 1 12-28-2010 10:38 PM
SIFT on the command line lamasmi Bioinformatics 2 08-17-2010 09:32 AM

Reply
 
Thread Tools
Old 11-16-2010, 07:13 AM   #1
Pawan Noel
Junior Member
 
Location: Paris

Join Date: Nov 2010
Posts: 4
Default SAMtools command line ???

Does anyone have a quick list of the most used SAMtool command lines

I'm really new to using UNIX:Linux and I would greatly appreciate if someone could share a pdf/doc for the SAMtool commands

Thank you very much and hv a nice day

Pawan
Pawan Noel is offline   Reply With Quote
Old 11-16-2010, 07:40 AM   #2
ffinkernagel
Senior Member
 
Location: Marburg, Germany

Join Date: Oct 2009
Posts: 110
Default

Running samtools without an argument will list all commands available. Then running the command without further arguments will tell you its usage.
ffinkernagel is offline   Reply With Quote
Old 11-16-2010, 07:41 AM   #3
johnny
Member
 
Location: Germany

Join Date: Dec 2009
Posts: 15
Default

http://samtools.sourceforge.net/samtools.shtml
johnny is offline   Reply With Quote
Old 11-16-2010, 07:50 AM   #4
Richard Finney
Senior Member
 
Location: bethesda

Join Date: Feb 2009
Posts: 700
Default

Here's the basic workflow for most jobs. test1.sam is the output from your favorite alignment program. If not sam, you'll have to convert it SAM but many aligners are providing SAM output these days. The "export" command is a bash (bash is a common command line processor in UNIX/Linux) way of "aliasing" a longer command.

export SAM=/usr/joeuser/samtools-0.1.8/samtools

${SAM} view -b -S test1.sam > test1.presort.bam

${SAM} sort -m 5179869184 test1.presort.bam test1

${SAM} index test1.bam

${SAM} flagstat test1.bam > test1.rpt
Richard Finney is offline   Reply With Quote
Old 11-16-2010, 08:12 AM   #5
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

Probably you want to start reading the FAQ. Then move to reading the manual for each
action you want to use. Take your time for pileup.
__________________
-drd
drio is offline   Reply With Quote
Old 11-16-2010, 08:15 AM   #6
Pawan Noel
Junior Member
 
Location: Paris

Join Date: Nov 2010
Posts: 4
Default

Thank you very much guys .... I'll start with this info for now .... Have a nice evening Cheers
Pawan Noel is offline   Reply With Quote
Old 11-16-2010, 10:42 AM   #7
dawe
Senior Member
 
Location: 4530'25.22"N / 915'53.00"E

Join Date: Apr 2009
Posts: 258
Default

Not related to samtools, but I believe you should read these:
http://tldp.org/LDP/Bash-Beginners-Guide/html/
and
http://tldp.org/LDP/abs/html/
You can't go much far in UNIX/Linux without knowing the shell...

d
dawe is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:41 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO