How fix error "INVALID_MATE_REF_INDEX" in a SAM/BAM file of NGS data?

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5.0 years ago

zamani_2012 • 0

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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next-gen gatk SAM/BAM FILE • 675 views

ADD COMMENT • link updated 4.9 years ago by Biostar 20 • written 5.0 years ago by zamani_2012 • 0

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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 REPLY • link 5.0 years ago by Pierre Lindenbaum 161k

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Relevant links:

https://gatkforums.broadinstitute.org/gatk/discussion/7571/errors-in-sam-bam-files-can-be-diagnosed-with-validatesamfile

https://software.broadinstitute.org/gatk/documentation/article.php?id=7571

ADD REPLY • link 5.0 years ago by h.mon 35k

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