User error while using GATK SplitNcigarReads

Question

[jahanzaib119311]

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

Answer 1

[finswimmer]

• 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.

[jahanzaib119311]

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.