Is indexing .bam files before samtools mpileup necessary?

[MGCBrown]

Is indexing your .bam files a necessary step for running the samtools variant calling pipeline (ie samtools mpileup, bcftools view etc)?

I know that indexing your genome/transcriptome is a necessary step but I can;t figure out if my coordinate sorted .bam files need to be indexed as well.

Thank you!

[dpryan]

Yes, you must index the BAM file too.

[MGCBrown]

Thank you, Devon!