User error while using GATK SplitNcigarReads
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2.5 years ago

while running SplitNCigarReads of GATK tool I am facing the following error.

A USER ERROR has occurred: Badly formed genome unclippedLoc: Contig chr11_gl000202_random given as location, but this contig isn't present in the Fasta sequence dictionary

gatk • 798 views
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2.5 years ago
• What is the exact command you have used?
• Make sure you use the same reference in the command line as the one used for generating the bam file.
• Make sure the dict file for the reference is up to date.
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Thank you so much for your kind reply the command ran without any error. I had re-indexed the reference file and there was some issue with the dict file.