On Fri, Jan 13, 2017 at 03:16:59PM -0800, Irena Fischer-Hwang wrote:
> 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.
It's very unli
Thanks Tommy for the estimate.
Thomas, you're right--I was inaccurately describing my workflow wishlist. I
am indeed indexing the BAM file before converting to SAM and then sorting
the SAM.
Peter: for experimental purposes.
On Sat, Jan 14, 2017 at 10:50 AM, Peter Cock
wrote:
> On Fri, Jan 13,
On Fri, Jan 13, 2017 at 11:16 PM, Irena Fischer-Hwang
wrote:
> Hi, I'm trying to index a huge BAM file (~180 GB) in anticipation of
> converting it to SAM.
Really?
If you already have a very large BAM file, why would you want
to turn it into a much much larger SAM file? Any relevant tools
ought
: Irena Fischer-Hwang mailto:ihw...@stanford.edu>>
> Date: Friday, 13 January 2017 23:16:00
> To:
> "samtools-help@lists.sourceforge.net<mailto:samtools-help@lists.sourceforge.net>"
>
> mailto:samtools-help@lists.sourceforge.net>>
> Subject: [Samtool
ailto: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
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 fu
