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
SAMtools pileup output zippered_ohio Bioinformatics 1 09-08-2011 01:27 PM
pileup output different using Maq and Samtools commands mr_boourns Bioinformatics 1 03-31-2011 03:05 AM
samtools pileup output file charlie_sequencing Bioinformatics 1 02-10-2011 12:51 PM
samtools pileup output for SNP detection Mansequencer Bioinformatics 1 09-08-2010 06:36 PM

Reply
 
Thread Tools
Old 09-26-2011, 02:49 PM   #1
shuang
Senior Member
 
Location: IL

Join Date: Jul 2011
Posts: 100
Default output info from samtools pileup?

When I piled up an alignment by this command, I received the result in the bottom. What does each column mean? I know "chr_2 5554123" is a SNP.


samtools pileup -c -f ../../ssahaSNP_result/Sorbil.fasta test.bam > test.full.pileup



chr_2 5554119 t T 30 0 60 1 . R
chr_2 5554120 t T 30 0 60 1 . P
chr_2 5554121 t T 30 0 60 1 . A
chr_2 5554122 g G 30 0 60 1 . A
chr_2 5554123 t C 0 2 60 1 C A
chr_2 5554124 a A 30 0 60 1 . X
shuang is offline   Reply With Quote
Old 09-26-2011, 04:35 PM   #2
zippered_ohio
Junior Member
 
Location: USA

Join Date: Jun 2011
Posts: 6
Default

Hi shuang,

You can find more information about the pileup command, its input and output, etc. here.

You have used the consensus ("-c") option, which will call a consensus base according to the MAQ model for each base.

There is more information about each of these columns here:

Quote:
"When consensus calling is switched on, pileup command will insert the consensus base, consensus quality, SNP quality and maximum mapping quality of the reads covering the sites between the `reference base' and the `read bases' columns."
zippered_ohio 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 03:21 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO