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Question: How fix error "INVALID_MATE_REF_INDEX" in a SAM/BAM file of NGS data?
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Hi everyone, I work on some NGS data using GATK package. However during working with various tools in GATK, I encountered error "INVALID_MATE_REF_INDEX"? What is is meaning of this error and How can I fix it?

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mate read is unmapped but it is associated to a chromosome.

How can I fix it?

depends of your version of gatk.

ADD REPLYlink 10 months ago
Pierre Lindenbaum
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