SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
output info from samtools pileup? shuang Bioinformatics 1 09-26-2011 04:35 PM
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 02-08-2011, 01:21 AM   #1
pravee1216
Member
 
Location: India

Join Date: Aug 2010
Posts: 35
Thumbs down No output from Samtools pileup

I tried to call consensus using samtools pileup from the filtered BAM file which has only reads with no mate. But the result was empty. The following is what I did:

1) From the complete BAM, I extracted reads (mapQV >8) which have no mate (mate unmapped) using "samtools view -f 0x8" - There are ~35m reads.
2) removed all duplicate reads using Picard
3) provided this filtered file to samtools for consensus calling with options "-c", "-Q 8", "-f ref.fas" ( i tried -m, -M as well)

Question here is 1) Why does pileup fail to call consensus 2) Did i make any mistake or do I modify any parameters 3) Is there any other tool can do this?

Any light to this will be a great help.

Thanks.

Praveen
pravee1216 is offline   Reply With Quote
Old 12-05-2012, 03:59 AM   #2
ekg
Member
 
Location: Boston, MA

Join Date: Apr 2010
Posts: 36
Default

Some tests I just did show that samtools mpileup only works for proper pairs. Can anyone else confirm this?

I was not able to call any variants until I marked the pairs with bamtools resolve.
ekg is offline   Reply With Quote
Reply

Tags
samtools pileup

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 10:05 PM.


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