I am currently working with one of Illumina's older Bam files and trying to run SamTools Pileup.  Unfortunately, the server has repeatedly timed out on me and I am unable to run the program on my file.  I was wondering if other people are having trouble running Samtools on human genome .bam files or whether this is secondary to the way the file is configured (i.e. it was first run through Illumina's proprietary software and provided as a .bam without an accompanying fastq file)?

Thanks for your help!

Jessie