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Sequence dictionaries are not the same size (613, 0) when trying to merge BAMs with MergeSamFiles

sp580sp580 GermanyMember
edited February 2019 in Ask the GATK team


I get the error Sequence dictionaries are not the same size (613, 0) when trying to merge 4 BAMs using the following expression:

SAMPLE_BAMs_RG=$(ls -1 $TMP/*.bam | grep $SAMPLE | sed 's/\/projekte/I=\/projekte/g') #this adds "I=" before the BAM path/name

java -jar $PICARD/picard.jar MergeSamFiles \
        $(echo $SAMPLE_BAMs_RG) \ # passing all BAMs at once
        O=$TMP/$SAMPLE.RG.merged.sorted.bam \

I am not sure what I am missing since there is no flag to specify the dictionary path.

Thanks in advance


Best Answer


  • shleeshlee CambridgeMember, Broadie ✭✭✭✭✭

    Hi @sp580,

    The tool equates the @SQ lines in the header of the BAM as the sequence dictionary. You will want to check that these are identical for your BAMs.

  • sp580sp580 GermanyMember

    Thanks @shlee
    the @SQ lines are identical among the 4 BAMs I am passing to the tool

    However, there are 613 sequences (@SQ), which I guess is what the error message is also indicating (although I do not get the "0").

    Are there too many sequences in the reference?

  • sp580sp580 GermanyMember

    Thanks @shlee
    the problem was that the input expression was catching another bam which was empty.

    After correcting this, the tool worked. Sorry for using your time :( ... at least now I understand that this error exists and what it means.


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