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jandrewrfarrell / RUFUS

RUFUS k-mer based genomic variant detection
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Running time when using CRAM input #22

Open mkohailan opened 2 years ago

mkohailan commented 2 years ago

Hi, I tried the latest version of RUFUS to run CRAM files (because the -cr option was not available in the version I have from 2018).

However, the run takes almost a week to finish, while it takes only overnight with BAMs.

Any thoughts on this?

jandrewrfarrell commented 2 years ago

Glad Rufus has been working for you, sorry about the slowdown, there’s definitely something off it shouldn’t take that long. The —cr option should not slow down Rufus that much, all it really does is change the samtools command used to read the files. What type of data are you during, whole genome or exome? Can you send me an example of your command line?

================================= Andrew Farrell PhD
Director of Research and Science Department of Human Genetics
USTAR Center for Genetic Discovery
Eccles Institute of Human Genetics
University of Utah School of Medicine​ 15 North 2030 East, Room 7140
Salt Lake City, UT 84112-5330
Email: @.*** http://marthlab.org/

On Aug 7, 2022, at 1:25 AM, mkohailan @.***> wrote:

 Hi, I tried the latest version of RUFUS to run CRAM files (because the -cr option was not available in the version I have from 2018).

However, the run takes almost a week to finish, while it takes only overnight with BAMs.

Any thoughts on this?

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