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Old 11-16-2012, 12:15 PM   #1
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, 03:26 PM   #2
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Location: stanford

Join Date: Jul 2014
Posts: 1

I also have the same issue, have you been able to resolve it?
miguelmata is offline   Reply With Quote
Old 04-14-2018, 12:12 AM   #3
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Location: Finland

Join Date: Oct 2012
Posts: 2

By default the tool requires an exact match -- to relax that requirement, use ALLOW_INCOMPLETE_DICT_CONCORDANCE=TRUE
Vandelnokk is offline   Reply With Quote

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