I used GATK and Mummer to call INDEL, final results were good but it doesn't match with wet lab marker INDEL.
Out of five markers, it matches only one, could anyone help me to solve this issues.
Please use appropriate tags. Your question is about InDels, GATK and Mummer. These should have been added as tags when you created the question. When you add appropriate tags, users that follow the tag (usually experts interested in helping others in that subject matter) get notified of your question, and this means you stand a better chance at getting a relevant, useful response faster.
If you explain in more detail what you did (including commands) on the GATK forum we can try to help you. https://gatkforums.broadinstitute.org/gatk
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