How fix error "INVALID_MATE_REF_INDEX" in a SAM/BAM file of NGS data?
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.
depends of your version of gatk.
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