Hi Irena,
It should require less than 100MB of memory to index a bam file. Perhaps you
ran into run time restrictions instead?
Cheers,
Tommy
From: Irena Fischer-Hwang <ihw...@stanford.edu<mailto:ihw...@stanford.edu>>
Date: Friday, 13 January 2017 23:16:00
To:
"samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>"
<samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>>
Subject: [Samtools-help] indexing huge BAM file
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
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