Reference is not provide

[Larrycpan]

Thanks for the contribution. I'm using the command
samtools mpileup -BQ 0 -d 10000 -f GRCh38.primary_assembly.genome.fa -q 40 -b filenames.txt | monovar.py -p 0.002 -a 0.2 -t 0.05 -m 10 -f GRCh38.primary_assembly.genome.fa -b filenames.txt -o output.vcf.
Then the error appears:
print "Error: Reference genome file not provided. Use '-f' for reference genome file.\n
What's the problem? thx!

[dklimes]

I'm sure this is way too late, but I'll write this for the sake of it. I encountered the same issue where even when I passed the fasta file it didn't find it. The reason, I found, is in the version of python I was using. I could only make MonoVar work when running python 2.6 or 2.7.