SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Using SNP/Indel Callers with 454 adaptivegenome Bioinformatics 6 05-18-2012 01:13 PM
SNP/Indel analysis and homopolymer errors gavin.oliver General 3 11-10-2011 06:57 AM
SNP and indel calling methods Rachelly Bioinformatics 1 11-24-2010 03:45 AM
ROAST software for SNP/InDel ntremblay Bioinformatics 0 07-19-2010 09:39 AM
Is there any package available for SNP/Indel annotation? Ling Bioinformatics 3 01-28-2010 08:58 AM

Reply
 
Thread Tools
Old 12-17-2011, 04:28 PM   #1
murphycj
Member
 
Location: Wisconsin

Join Date: Sep 2011
Posts: 10
Default SNP/indel quality

Hi,

Aim:
I' am comparing mpileup/bcftools and UnifiedGenotyper.

My data:
7 samples. Reads aligned with tophat against hg19.

Result:
Average 'QUAL' in vcf files: UnifiedGenotyper (404), mpileup/bcftools (28).
Average snp/indel calls: UnifiedGenotyper (49,739), mpileup/bcftools (253,933).

Issue:
Greater than 90% of the tophat-mapped reads had MAPQ of 255. Therefore, when using UnifiedGenotyper, I had to use:"-rf ReassignMappingQuality -DMQ 60".

Question:
Can I compare the 'QUAL' field in the vcf output call sets from GATK and SAMtools? My intuition says no. However, I realize GATK uses MAPQ as a cap on base quality. So if anything, the 'QUAL' values for GATK calls are low. I' am still looking into how the SNP/indel calling algorithms use MAPQ.

Any input would be helpful. I' am a novice. Also, I should maybe redo the tophat alignment for correct MAPQ.

Best.
murphycj 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 07:36 PM.


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