I intend to know the base frequencies at each positions in my BAM files. For the same, I am using samtools mpileup script, which can serve the purpose. While running the script, I am encountering an error which is not understandable by me. So I am reaching out to all the expert bioinformaticians for their assistance. I have posted the error below for your reference:
/Users/Desktop/Tools/samtools-1.3/samtools mpileup -f GCF_000184105.1_Geom_destructans_V1_genomic.fa -r supercont1.1-supercont1.1847 712206_realigned_reads.bam N_american_realigned_reads.bam Nova_Scotia_1_realigned_reads.bam
[E::mpileup] fail to parse region 'supercont1.1-supercont1.1847' with 712206_realigned_reads.bam
Thank you in advance.