SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
No output from Samtools pileup pravee1216 Bioinformatics 1 12-05-2012 03:59 AM
output info from samtools pileup? shuang Bioinformatics 1 09-26-2011 04:35 PM
SNP quality score in Samtools pileup wangzkai Bioinformatics 5 09-21-2011 06:32 AM
SAMtools pileup output zippered_ohio Bioinformatics 1 09-08-2011 01:27 PM
How is SNP quality calculated in SAMTOOLS pileup? lazyworm Bioinformatics 2 05-28-2010 12:00 AM

Reply
 
Thread Tools
Old 09-08-2010, 07:56 AM   #1
Mansequencer
Member
 
Location: Canada

Join Date: Jul 2010
Posts: 16
Default samtools pileup output for SNP detection

Hi All,
I aligned 50 bp solexa reads onto a reference genome using bowtie and now I am using samtools pileup -vcf to call SNPs. This is the output it generates:
scaffold179 29989 T A 30 30 60 1 A B
scaffold179 29991 A G 4 4 60 1 G #
scaffold179 29992 A T 4 4 60 1 T #
scaffold179 29993 T A 4 4 60 1 N #
scaffold179 29994 T A 4 4 60 1 N #
scaffold179 29995 A C 4 4 60 1 C #
scaffold179 29997 T A 4 4 60 1 N #
scaffold179 29998 G C 4 4 60 1 C #
scaffold179 29999 T C 4 4 60 1 C #
scaffold179 30000 T A 4 4 60 1 N #
scaffold179 30001 T A 4 4 60 1 A #
scaffold179 30002 G A 4 4 60 1 A #
scaffold179 30003 A G 4 4 60 1 G #
scaffold179 30004 T C 4 4 60 1 C #
scaffold179 30005 T A 4 4 60 1 A #
scaffold179 30006 T A 4 4 60 1 N #
scaffold179 30007 G A 4 4 60 1 N #
scaffold179 30008 T A 4 4 60 1 N #
scaffold179 30009 G A 4 4 60 1 N #
scaffold179 30010 T A 4 4 60 1 N #
scaffold179 30011 T A 4 4 60 1 N #
scaffold179 30012 T A 4 4 60 1 N #
scaffold179 30013 T A 4 4 60 1 N #
scaffold179 30014 G A 4 4 60 1 N #

I understand that columns from left to right are:
Scaffold name:
coordinate:
reference base:
polymorphic base:

I am confused about the numbers after the 4th column. Please suggest as to what they correspond to.
Also when I try to look at the alignment in tview, it shows only Ns after the first 80 pb. My reference genome does contain some short stretches of Ns but is not all Ns so why does the samtools tview shows only Ns?
Any suggestion would be highly appreciated.
Thanks for all the help.
Thanks.
Mansequencer is offline   Reply With Quote
Old 09-08-2010, 06:36 PM   #2
qtrinh
Member
 
Location: Canada

Join Date: May 2008
Posts: 20
Default

Here is a link that describes the output of consensus and indels calling: http://samtools.sourceforge.net/cns0.shtml
qtrinh 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 08:58 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO