Extremely Slow BisulfiteGenotyper

[bruce moran]

Hi,

I have been testing bisulfite conversion efficiency using MiSeq and have multiple small samles, ~1m PE 75bp reads. I use a pipeline:

1. Trimmomatic, Bismark
   
2. Sort, Reorder, Remove Duplicates
   
3. BisulfiteCountCovariates
4. BisulfiteTableRecalibration
5. BisulfiteGenotyper

Up until 5, everything is fine, my conversions work well and we are happy to go on to capture and run on HiSeq. However, I was interested to test BisSNP for calling SNPs, and included it in the pipeline therefore. I have used GATK on exomes, and I have never seen it run so slowly. Example: I left a run 90 hours, 1.3% complete for 200,000 reads... No errors thrown, I am using a very large dbSNP VCF but even when this is not included I see this behaviour. I am using BisSNP-0.82.2.jar.

Any ideas on what is going on would be appreciated.

Also, in your manual you show plot of recalibration, but there is no script to generate the plots, only to make the data. Do you have something publically available to make plots that you can share? Just to save me a little time=)

Thanks for all your work on BisSNP,

Bruce.

[ping]

Hi Bruce,

Large dbSNP usually is not a problem. But large sample size could be a problem. Have you test it with just one sample bam file?

In user manual, there is a section (4.4.4 Generate recalibration plot) about how to generate plot from the output file.

let me know if you have further question

yaping

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Yaping Liu, Ph.D.

Postdoctoral Associate

Manolis Kellis Lab

Computer Science and Artificial Intelligence Lab (CSAIL)
Massachusetts Institute of Technology

Broad Institute of MIT and Harvard

Office Phone: +1 617 324 8436 
Email: 

lypin...@gmail.com

yap...@mit.edu

lyp...@broadinstitute.org

[bruce moran]

Hi Yaping,

yes, I have tested on single sample, it is still running very, very slowly, so slow as to be totally unusable. Any updates recently that may cause this? Do you have a test sample I can try to see if it is an issue with my installs?

Will take a look at the plot section,

Thanks,

Bruce.