This is a test version of Biostars. For the public version, visit https://www.biostars.org.
User error while using GATK SplitNcigarReads

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
• 2,264 views • link
written by jahanzaib119311 • jahanzaib119311

1 answer

  • 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.
• 0 views • link
written by finswimmer finswimmer

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.

• 0 views • link
written by jahanzaib119311 • jahanzaib119311

Log in to answer this question.

More posts like this