SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
ReorderSam.jar problem wijota Bioinformatics 2 11-10-2014 05:26 AM
Picard: problem with Java? aleidenroth Bioinformatics 9 06-29-2013 07:37 PM
Problems Running Picard's ReorderSam tatinhawk Bioinformatics 3 08-26-2012 07:57 PM
ReorderSam.jar in picard and GATK wisekh Bioinformatics 0 12-12-2011 07:27 AM
picard reOrder problem seq_GA Bioinformatics 2 11-21-2011 12:34 PM

Reply
 
Thread Tools
Old 11-16-2012, 11:15 AM   #1
twotwo
Member
 
Location: Ohio

Join Date: May 2012
Posts: 40
Default PICARD/ReorderSam reference problem

I got the sam file from the tophat with UCSC reference. Then I ran PICARD/ReorderSam with the reference from UCSC, which downloaded from the tophat website. And the reference folder contained .fa, .dict and .fa.fai. However the ReorderSam always gave me error message.

Here is my code:
java -jar /home/software/picard-tools-1.79/ReorderSam.jar I=/mnt/mutation/bamfile/sample1_f.bam O=/mnt/mutation/bamfile/sample1_sorted_reorder.bam R=/home//reference/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa

Here is the error message:

Exception in thread "main" net.sf.picard.PicardException: New reference sequence does not contain a matching contig for chr11_gl000202_random

Any comments on that???
twotwo is offline   Reply With Quote
Old 11-11-2014, 02:26 PM   #2
miguelmata
Junior Member
 
Location: stanford

Join Date: Jul 2014
Posts: 1
Default

I also have the same issue, have you been able to resolve it?
miguelmata is offline   Reply With Quote
Old 04-13-2018, 11:12 PM   #3
Vandelnokk
Junior Member
 
Location: Finland

Join Date: Oct 2012
Posts: 2
Default

By default the tool requires an exact match -- to relax that requirement, use ALLOW_INCOMPLETE_DICT_CONCORDANCE=TRUE
Vandelnokk 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 08:29 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO