Hi everyone,
I was running the following comand line:
java -jar /home/Picard/picard.jar CollectAlignmentSummaryMetrics -R GRCh38.fna -I 2H.bam -O output2H.txt
but I got the following error:
Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (194, 639) at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:259) at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:342) at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:328) at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:117)
I am sure that the reference genome I gave in input is the same reference genome used to align and obtain the BAM file. Actually, I've just figured out that the sam header and the referencegenome.dict header are not the same. In particular, SAM's header is version 1.5, while referencegenome.dict's header is version 1.6. How can I make them consistent? So, how can I make them have the same header?
Thanks in advance.
