The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Get notifications!


You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

Got a problem?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block as demonstrated here.

Jump to another community
Download the latest Picard release at https://github.com/broadinstitute/picard/releases.
GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

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
Tagged:

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    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.

Sign In or Register to comment.