SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
NO indel output from Samtools by using nearly default settings wwmm933 Bioinformatics 1 12-05-2012 04:18 AM
error during GATK indel realigner david.tamborero Bioinformatics 6 07-18-2012 06:30 AM
gatk indel calling problem Alex Renwick Bioinformatics 6 12-02-2011 12:25 PM
GATK indel raligner after bfast alignement david.tamborero Bioinformatics 4 11-21-2011 10:18 AM
problem about GATK indel VQSR wanguan2000 Bioinformatics 2 11-07-2011 07:15 AM

Reply
 
Thread Tools
Old 10-19-2011, 08:01 AM   #1
inou13
Junior Member
 
Location: uk

Join Date: Sep 2010
Posts: 4
Default GATK indel settings help please

Dear all,
I am new to GATK and try to test this to look at indels from ILLUMINA nextGen data generated from custom pull down experiments. I have 2 set of files, one "disease" file and one "no-disease"( from the same individual). I know from other experiments that there is a 4pb duplication in the disease sample, I found it as well using SAMTOOLS pileup .

I wanted to try GATK on the same set of samples and get indels using SomaticIndelDetector.
I have tried without local realignment first
java -Xmx2g -jar GenomeAnalysisTK.jar \
-R ref.fasta \
-T SomaticIndelDetector \
-o indels.vcf \
-verbose indels.txt
-I:normal normal.bam \
-I:tumor tumor.bam

from the output vcf I cannot detect my duplication, I have tried as well in the single file mode (without putting a normal reference file).

I tried to realign using both RealignerTargetCreator and IndelRealigner. It appears that this region is called in the RealignerTargetCreator as it is a bit complex.
I used this for my disease file and did the same thing for the normal file
java -Xmx2g -jar GenomeAnalysisTK.jar \
-I input.bam \
-R ref.fasta \
-T RealignerTargetCreator \
-o forIndelRealigner.intervals \

then I ran IndelRealigner for both files, using the just created forIndelRealigner.intervals .
java -Xmx4g -jar GenomeAnalysisTK.jar \
-I input.bam \
-R ref.fasta \
-T IndelRealigner \
-targetIntervals intervalListFromRTC.intervals \
-o realignedBam.bam \

With my new realigned Bams I did re-run SomaticIndelDetector , and did not detect any duplication, this region is not called. I have tried as well in the single file mode (without putting a normal reference file), no calls.

I have checked that this region is not discarded ( as containing too few or too much reads ) ..

Could you please help/advise for better settings?
Many thanks
inou13 is offline   Reply With Quote
Old 10-19-2011, 11:31 AM   #2
RDW
Member
 
Location: London

Join Date: Oct 2008
Posts: 63
Default

Quote:
Originally Posted by inou13 View Post
With my new realigned Bams I did re-run SomaticIndelDetector , and did not detect any duplication, this region is not called. I have tried as well in the single file mode (without putting a normal reference file), no calls.
Have you also tried the UnifiedGenotyper in indel mode on the realigned 'disease' file? (I think the SID is basically the old Indel Genotyper V2, and I get the impression they only keep it in GATK because it has the somatic mode that the UG lacks).
RDW is offline   Reply With Quote
Old 10-25-2011, 09:09 AM   #3
inou13
Junior Member
 
Location: uk

Join Date: Sep 2010
Posts: 4
Default

HI, thanks for your tip, I can find an indel now 5 pb near where my indel is supposed to be, so somewhat not the sequence and position I expected ... could it be due to the realignment?
this is the command line I have used for UG
-jar GenomeAnalysisTK.jar -R /l.fa -T UnifiedGenotyper -l INFO -glm INDEL -o indels_UG.vcf -I /realigned.bam
thanks
inou13 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 02:58 PM.


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