gatk genome loc coordinates exceed the contig size. While trying to run genomicsdbimport

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Paulo Ricardo

• June 09, 2024 09:43

REQUIRED for all errors and issues:  
a) GATK v4.4.0.0
b) Exact command used: gatk GenomicsDBImport -R GRCm39.primary_assembly.genome.fa -L interval.bed --genomicsdb-workspace-path ./DB -V CD19CTRL.vcf.gz
c) Entire program log: A USER ERROR has occurred: Badly formed genome unclippedLoc: Parameters to GenomeLocParser are incorrect:The genome loc  coordinates 195154803-195155042 exceed the contig size (195154279) 

My reference is mm10 and the bed file I'm using is from

ureSelect Mouse All Exon V1

Design ID: S0276129 Species: M. musculus Build Version: UCSC mm9, NCBI Build 37, July 2007 I don't know if the problem is related to differente references being used, but of course i would like to use the most recent one, however my bed file was supplied by chemagilent to get the interval list required, and they only of this reference.

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  Gökalp Çelik

  • June 09, 2024 10:08

  Hi Paulo Ricardo

  You need to use what ever genome fasta file used to capture variants from reads to import into GenomicsDB. Any incompatibilities will result in these errors. 

  You can check contig sizes from the sequence dictionary file. If your bed file coordinates exceed those lengths then you will receive this error. 

  Make sure that your VCF sequence dictionary is compatible with your fasta dictionary otherwise you will not get any results. 

  Regards. 

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  Paulo Ricardo

  • June 09, 2024 10:49

  Hello, thank you for the fast response.

  But the interval list should be the bed file provided by the manufacturer of the sequencing right? I used the same reference to create the vcf file of the normal sample, and i'm using the same in the parameter -R for genomics DB import. How can I do that with this bed file?

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  Paulo Ricardo

  • June 09, 2024 10:53

  My doubt is in the parameter -L, how do I provide the interval list? In one of the foruns I saw that I could use the covered.bed file provided by the manufacturer. So I use it, after putting it in the correct format of "chr" "start" "end"

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  Gökalp Çelik

  • June 10, 2024 15:44

  Hi Paulo Ricardo

  You don't have to use the bed file from any manufacturer for GenomicsDB import, although you can use it but it is not necessary. You can use whole contig names as values for -L therefore you may import in parallel into multiple GenomicsDB instances. 

  If the bed file from the manufacturer is not compatible with the reference genome such as having intervals exceeding the size of the contig, you may get such messages. You need to check with the manufacturer's fact sheets to ensure these compatibilities. 

  Regards. 

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