Question: using GATK UnifiedGenotyper on a single chromosome
gravatar for stefano.iantorno
5.1 years ago by
United Kingdom
stefano.iantorno70 wrote:


I am trying to run GATK UnifiedGenotyper on a single chromosome from a 30+ chromosome genome.

I have tried feeding GATK the bam file (containing reads for all chromosomes plus some scaffolds) and a fasta file of only the one chromosome I want variants for. However I receive the following error:

ERROR MESSAGE: Badly formed genome loc: Contig Scaffold143 given as location, but this contig isn't present in the Fasta sequence dictionary

Where Scaffold143 is one of the unassembled scaffolds.

I am assuming that the error comes from the bam file containing reads for that scaffold? How do I solve this? I somehow stumbled upon the -L argument for UnifiedGenotyper but I could not find any documentation for it on the GATK website. Is this an argument that defines the boundaries of a region on which to call variants? If so, this could be a way to work around the problem generated by feeding GATK only the fasta file of the chromosome I'm interested in.



java gatk genome • 2.7k views
ADD COMMENTlink modified 4.5 years ago by Biostar ♦♦ 20 • written 5.1 years ago by stefano.iantorno70

In case you want to call variants for one chromosome you can use "-L" or "Intervals of interest" parameter in GATK. You can give an input file that will have <chr>:<start>-<stop> for your chromosome of interest. This way GATK Unified genotyper will call variants for only that chromosome.

ADD REPLYlink modified 5.1 years ago • written 5.1 years ago by Ashutosh Pandey11k
gravatar for Paweł Sztromwasser
5.1 years ago by
University of Bergen, Norway
Paweł Sztromwasser20 wrote:

You are right. If the bam contains reads mapped to position that is not present in your (filtered) reference, GATK will complain. As you also noticed, you can use the -L parameter of GATK. The documentation is here:

Remember to provide as the reference the same file that was used for mapping (all chromosomes and scaffolds)


ADD COMMENTlink written 5.1 years ago by Paweł Sztromwasser20
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