Question: bwa mem -K 100000000
0
gravatar for gwotto
11 days ago by
gwotto0
gwotto0 wrote:

Hi,

in Regier et al.: "Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects", bioRxiv, doi 10.1101/269316 The use bwa mem in their alignments with the option '-K 100000000'. Also in https://github.com/CCDG/Pipeline-Standardization/blob/master/PipelineStandard.md it is noted: '-K 100000000 to achieve deterministic alignment results (Note: this is a hidden option)'. I could not find any more detailed description of this option. Does anyone know what it does and where this is documented? Thanks a lot!

alignment next-gen • 105 views
ADD COMMENTlink written 11 days ago by gwotto0

if it is a 'hidden' option as you say, it will have very little to no documentation (or it would not have been hidden)

ADD REPLYlink written 11 days ago by lieven.sterck2.4k
3
gravatar for genomax
11 days ago by
genomax55k
United States
genomax55k wrote:
 -K INT        process INT input bases in each batch regardless of nThreads (for reproducibility) []

It is included in inline help for bwa mem.

ADD COMMENTlink written 11 days ago by genomax55k

I stand corrected.

but it does not seem to be as hidden as described then (though it apparently is not present in the 'online' doc)

ADD REPLYlink written 11 days ago by lieven.sterck2.4k
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