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.