[Samtools-help] indexing huge BAM file

[Irena Fischer-H. <ih...@st...>]

Hi, I'm trying to index a huge BAM file (~180 GB) in anticipation of
converting it to SAM. I tried running

>> samtools index file.bam

but it got killed, most likely because my computer ran out of RAM. Can
someone give me a ballpark estimate of how much memory is needed to index a
BAM file as a function of the BAM file's size? Correspondingly, what sort
of memory requirements should I anticipate in order to convert the indexed
BAM file to a sorted SAM file?

Thanks,
-Irena