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picard CalculateHSMetrics error

I'm trying to run picard CalculateHSMetrics step on a bam file to get hybrid selection metrics and per target coverage across a list of target and probe intervals.

I get the below error,

SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (87, 85)

I checked if the @SQ header lines in my bam and interval files are the same, and they are. Is it essential that the header of bam and interval files match exactly?

picard metrics
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updated by mastal511 mastal511 • written by Kssr Kssr

1 answer

This is complaining about sequence dictionaries. Do your files have .dict indexes? It looks like that is what it is complaining about.

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written by mastal511 mastal511

I understand the error is about sequence dictionaries. Yes, my files -bam and target & probe intervals have .dict indexes. I'm not sure what the error message implies, @SQ lines in the header of files are same. Only difference is my bam has GO:none in the @HD line and @PG lines(which I think is okay). Is the error due to having GO:none in the @HD line of my bam? Appreciate any help.

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written by Kssr Kssr

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