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about an error using DepthOfCoverage with -geneList

gpleogpleo Member
edited January 2013 in Ask the GATK team

when " RMDTrackBuilder - Loading Tribble index from disk for file refGene.sorted.txt "
error occurs:

ERROR MESSAGE: Badly formed genome loc: Contig chr1 given as location, but this contig isn't present in the Fasta sequence dictionary

is it means that my refGene.sorted.txt or b37.fasta file is badly formed?
what should I do ?

Post edited by Geraldine_VdAuwera on
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Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    Each file is probably fine independently, but the error means there is a mismatch between them (specifically, how contigs/chromosomes are named). You're probably using the wrong reference fasta file.

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