I am using bam-readcount. However, when I run the following input I get a blank output;
$ bam-readcount -f NCBI_ReferenceGenome.fna -l decomposed.vcf Bowtie2.bam [-b 20] > output.readcount
After running the script, I get the following;
Minimum mapping quality is set to 0 Expect library: Bowtie2 in BAM
The documentation says the output should be a tab-delimited file with column names, however output.readcount is empty. Assuming maybe my files are the problem, I should still get the column names in the output, right? I am a novice and am not sure where to look further in troubleshooting.
Thank you for your help