Question: Pindel too slow. How to speedup
gravatar for chris
3.6 years ago by
chris40 wrote:


I aligned five 5x mate-pair libraries with different insert sizes to a 300M genome and started Pindel without the dispersed duplicates option on all BAM files. It's running for 10 days now on 30 cores and processeced around half of the genome.

Is there a way to speed up Pindel? E.g. de-duplication? Is that the expected runtime?

I read about processing the chromosomes individually. How do you deal with interchromosomal duplication in that case?



pindel • 1.6k views
ADD COMMENTlink modified 3.6 years ago by Brian Bushnell15k • written 3.6 years ago by chris40
I have the same problem and would be interested in a solution.
ADD REPLYlink written 3.6 years ago by Christian2.6k

Same here.

ADD REPLYlink written 3.6 years ago by iraun3.3k
gravatar for liangkaiye
3.6 years ago by
United States
liangkaiye250 wrote:

Newest Pindel code? You could split by smaller segments (say 10MB) per job with 4 cores and this will not affect interchr prediction. 


If on exome data, I sometimes saw coverage spikes (several kx) in several narrow regions, this causes Pindel to slow down and have memory issue. You might use -J to exclude those regions. I have tried to solve this but have not found a smart way to handle huge coverage variation in the data. 



ADD COMMENTlink written 3.6 years ago by liangkaiye250
gravatar for Brian Bushnell
3.6 years ago by
Walnut Creek, USA
Brian Bushnell15k wrote:

If you are interested in indels, I suggest trying BBMap.  It allows alignment across long indels so you can detect them in a simple mapping+pileup rather than using an expensive realignment.  It also allows an arbitrarily large number of indels or substitutions per reads, so has very high sensitivity to multiple events.

Note - while it can detect deletions of arbitrary length (depending on the 'maxindel' flag), it cannot detect insertions more than ~50% of read length, since it only uses information from individual reads.  So it's not a complete replacement for Pindel.

ADD COMMENTlink written 3.6 years ago by Brian Bushnell15k
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