Hi, I am trying to do variant calling using bcftools both for mpileup and calling. I have around 60 bam files that were mapped using bwa-mem to my reference genome that contains 92 scaffolds.

I tried doing it all at once but after 30 days it only went through 20 out 92 scaffolds. What I want to do now is to do my variant calling by each scaffold and then merge all of my vcf files...

I tried with -r but I get an error:

[mpileup] fail to load index for ind1.bam Failed to open -: unknown file type.

Has anyone done this using bcftools?

Thank you for your help :).