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there are two examples. The first runs fine. The second generates this error
MESSAGE: Bad input: We encountered a non-standard non-IUPAC base in the provided reference: '10'
but the input files are the same. I only changed "Reads" to "Loci" in the command. I am running Unix so I do not need to retype the entire command. This command works fine
java -jar GenomeAnalysisTK.jar -T CountReads -R exampleFASTA.fasta -I exampleBAM.bam
This command produces the error
java -jar GenomeAnalysisTK.jar -T CountLoci -R exampleFASTA.fasta -I exampleBAM.bam -o output.txt