SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Qubit library quantitation variations Smriti Sample Prep / Library Generation 5 11-02-2013 09:57 AM
Structural variations using Newbler mapper Soni Bioinformatics 2 12-06-2011 09:58 PM
Identifying variations from one sample dingxiaofan1 Bioinformatics 2 08-17-2011 01:59 PM
Reproducible variations of accuracy Michael L. Altshuler Illumina/Solexa 0 10-09-2010 02:21 AM
Structural Variations sparks Bioinformatics 0 10-30-2008 02:16 PM

Reply
 
Thread Tools
Old 02-17-2011, 08:28 AM   #1
JohnK
Senior Member
 
Location: Los Angeles, China.

Join Date: Feb 2010
Posts: 106
Default Variations off GATK

I have some Illumina data mapped via BowTie. Looking to call variations using the UnifiedGenotyper from GATK, but I keep getting this error:

Missing read group for read HWI-EAS392_0029_FC:4:95:12241:2946#ACTT

Any ideas?

Last edited by JohnK; 02-17-2011 at 08:36 AM.
JohnK is offline   Reply With Quote
Old 02-17-2011, 09:19 AM   #2
NGSfan
Senior Member
 
Location: Austria

Join Date: Apr 2009
Posts: 181
Default

Quote:
Originally Posted by JohnK View Post
I have some Illumina data mapped via BowTie. Looking to call variations using the UnifiedGenotyper from GATK, but I keep getting this error:

Missing read group for read HWI-EAS392_0029_FC:4:95:12241:2946#ACTT

Any ideas?

You need the add read groups to your SAM/BAM file. This was a pain in the butt in the beginning if you are not used to it - especially if you analyze only one sample at a time. I had to go back and redo all my analysis.The GATK have made it mandatory now.

Actually, it's a good idea to do anyway - helps you track your reads and helps with more complex downstream analysis. You need to look into adding it through the Bowtie command line (see the manual and help). Each program has a different way of doing it.

Basically it means adding a line to your SAM file, eg:

@RG ID:25291 SM:J00066 LB:LIB056 PL:illumina

The fields ID SM and LB are arbitary.. but PL: is sequencing platform specific and necessary.
NGSfan is offline   Reply With Quote
Old 02-17-2011, 11:21 AM   #3
JohnK
Senior Member
 
Location: Los Angeles, China.

Join Date: Feb 2010
Posts: 106
Default

Quote:
Originally Posted by NGSfan View Post
You need the add read groups to your SAM/BAM file. This was a pain in the butt in the beginning if you are not used to it - especially if you analyze only one sample at a time. I had to go back and redo all my analysis.The GATK have made it mandatory now.

Actually, it's a good idea to do anyway - helps you track your reads and helps with more complex downstream analysis. You need to look into adding it through the Bowtie command line (see the manual and help). Each program has a different way of doing it.

Basically it means adding a line to your SAM file, eg:

@RG ID:25291 SM:J00066 LB:LIB056 PL:illumina

The fields ID SM and LB are arbitary.. but PL: is sequencing platform specific and necessary.

Sweet! This sucks but thank you very much! Going to work on it now...
JohnK is offline   Reply With Quote
Reply

Tags
gatk

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 03:27 AM.


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