SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
paired-end, bam-file-format Azazel Bioinformatics 4 06-27-2012 11:09 PM
how to filter BWA paired-end alignments? guru Bioinformatics 2 08-24-2011 12:32 PM
Paired-end Bam from single-end aligned sam ramouz87 Bioinformatics 4 08-17-2011 12:55 PM
paired end fastq format in bwa Protaeus Bioinformatics 4 12-09-2010 02:28 PM
BWA and Overlapped Paired-End? Lee Sam Bioinformatics 1 06-08-2010 01:07 PM

Reply
 
Thread Tools
Old 12-07-2011, 11:45 AM   #1
oiiio
Senior Member
 
Location: USA

Join Date: Jan 2011
Posts: 104
Default Errors from Picard and GATK on a BWA paired-end BAM

I have two samples with the following errors. One had an error in Picard MarkDuplicates. The other in GATK IndelRealigner. Both samples were mapped using BWA on paired-end data.

Does anyone know of a way to resolve these errors without removing reads from the sample? Any input at all is greatly appreciated

In Picard:


Code:
Exception in thread "main" net.sf.picard.PicardException: Value was put into PairInfoMap more than once.  2: foo:USI-EAS034_4_PE1_FC304CLAAXX:2:22:534:490
	at net.sf.picard.sam.CoordinateSortedPairInfoMap.ensureSequenceLoaded(CoordinateSortedPairInfoMap.java:124)
	at net.sf.picard.sam.CoordinateSortedPairInfoMap.remove(CoordinateSortedPairInfoMap.java:78)
	at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:61)
	at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:294)
	at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:117)
	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
	at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:101)
and in GATK:

Code:
##### ERROR MESSAGE: Exception when processing alignment for BAM index USI-EAS034_2_PE_FC307TBAAXX:3:79:1633:1917 2/2 45b aligned read.
oiiio is offline   Reply With Quote
Old 12-07-2011, 01:44 PM   #2
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 901
Default

It would probably help if you showed all the .sam entries for reads with that name.
swbarnes2 is offline   Reply With Quote
Old 12-07-2011, 07:50 PM   #3
oiiio
Senior Member
 
Location: USA

Join Date: Jan 2011
Posts: 104
Default

I am searching for them, but these BAMs are quite large and it will require some time. In the meantime, do you have any thoughts on the problems?
oiiio 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 02:18 AM.


Powered by vBulletin® Version 3.8.6
Copyright ©2000 - 2014, Jelsoft Enterprises Ltd.