I am attempting to use the qualimap bamqc tool to get qc information and having a bit of trouble using it for testing of small inputs. I am running the following
qualimap bamqc -bam smalldata.bam -c -gd HUMAN -gff newbed.bed -outdir outfolder
Both the bam and the bed file are "small". i think it's obvious what that means for the bam. for the bed that means I extracted a few lines, in this case one from each chromosome. bamqc runs with no error but outfolder/raw_data_qualimapReport is empty and outfolder/genome_results.txt is much shorter. I instead attempted to use the original targets bed (Agilent SureSelect) and outfolder/raw_data_qualimapReport was populated and outfolder/genome_results.txt was much longer.
Why is this the case and is the minimum required content for the bed/gtf/gff defined anywhere? Again this is for quick testing so ideally I want to have the smallest possible bed file for this.
