Question: User error while using GATK SplitNcigarReads
gravatar for jahanzaib119311
5 weeks ago by
jahanzaib1193110 wrote:

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 • 95 views
ADD COMMENTlink modified 28 days ago • written 5 weeks ago by jahanzaib1193110

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.

ADD REPLYlink written 28 days ago by jahanzaib1193110

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ADD REPLYlink written 27 days ago by ATpoint21k
gravatar for finswimmer
5 weeks ago by
finswimmer12k wrote:
  • 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.
ADD COMMENTlink written 5 weeks ago by finswimmer12k
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