Hi, I am getting en error from CONVERT_MT_BAM_TO_FASTQ:GATK4_PRINTREADS_MT":gatk4 that says: "Badly formed genome unclippedLoc: Query interval "MT" is not valid for this input." Possibly relevant parameters that I set in the config file is: mito_name = 'MT' fasta = '/home/ubuntu/raredisease-configs/refData/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa' mt_fasta = '/home/ubuntu/raredisease-configs/refData/Homo_sapiens/NCBI/GRCh38/Sequence/AbundantSequences/chrM.fa' The genome fasta file used by the test config seems to have the MT sequence included in it so the mt_fasta parametewr does not need to be set what I understand. May this introduces some problem? Based on this does anyone some idea about what cause the error?

Turned out “chrM” and not “MT” was used in the genome.fa and the interval file. So using mito_name = ‘MT’ instead of the above worked. mt_fasta is not needed to be set.