Hi,
Is it possible to merge bam files from the same sample but different reference sequence and thus different headers, so that I work with one single alignment file instead of two?.
I tried
but I got the following error:
Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequences at index 0 don't match
Cheers,
Dave
p.s.: I must say that the MERGE_SEQUENCE_DICTIONARIES flag seems to be related to this task but I am not sure what it actually means
Is it possible to merge bam files from the same sample but different reference sequence and thus different headers, so that I work with one single alignment file instead of two?.
I tried
Code:
java -Xmx4g -jar ~/picard-tools-1.61/MergeSamFiles.jar INPUT=Sample1_exon1.bam INPUT=Sample1_exon2.bam OUTPUT=Sample1_merged.bam ASSUME_SORTED=true USE_THREADING=true VALIDATION_STRINGENCY=LENIENT
Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequences at index 0 don't match
Cheers,
Dave
p.s.: I must say that the MERGE_SEQUENCE_DICTIONARIES flag seems to be related to this task but I am not sure what it actually means
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