SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
samtools view -l/-r options oghabian Bioinformatics 1 06-21-2012 08:33 AM
samtools view seq_lover Bioinformatics 2 04-27-2012 11:22 AM
samtools view without header Gen2007 Bioinformatics 4 11-16-2011 09:58 AM
Question about samtools view -r? syedsaid Bioinformatics 0 09-29-2011 02:00 AM
Samtools view michalkovac Bioinformatics 2 07-19-2011 05:25 AM

Reply
 
Thread Tools
Old 07-06-2012, 01:15 AM   #1
Andrew Beckerman
Junior Member
 
Location: Sheffield, UK

Join Date: Apr 2012
Posts: 5
Default samtools view and mapq

I am working with paired end Illumina resequencing data from multiple populations.

My workflow involves samtools view -q to generate bamfiles with specific mapq score thresholds, samtools mpileup, and then a workflow specific to pooled DNA samples and multiple population comparisons (popoolation2), which identifies fst values for snps and more.

I have run into a confusing aspect of mapq scores (perhaps). When I use a mapq score of 10 to generate the bam-files, I recover substantial numbers of snps in my workflow. However, if I use 20, ALL of these disappear. I have examined the mapq scores at various snp locations from the data with the mapq score of 10, and given the read depth (correct term?), there are several mapq scores for each snp, most of which are >20.

I am basically interested in how samtools view -q 20 versus -q 10 "removes" particular locations from the bamfile - for it seems like a very steep threshold.

I hope this makes sense.
Andrew Beckerman is offline   Reply With Quote
Old 07-18-2012, 05:14 AM   #2
Andrew Beckerman
Junior Member
 
Location: Sheffield, UK

Join Date: Apr 2012
Posts: 5
Default

I sorted this.... it was a problem with -q arguments in different functions not matching.
Andrew Beckerman is offline   Reply With Quote
Reply

Tags
mapq, samtools options

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 08:18 AM.


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