Biostar Beta. Not for public use.
Question: How fix error "INVALID_MATE_REF_INDEX" in a SAM/BAM file of NGS data?
Entering edit mode

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?


Entering edit mode

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

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.0