Question: bwa mem -K 100000000
0
gravatar for gwotto
4 months 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 • 222 views
ADD COMMENTlink written 4 months 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 4 months ago by lieven.sterck3.5k
4
gravatar for genomax
4 months ago by
genomax60k
United States
genomax60k 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 4 months ago by genomax60k

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 4 months ago by lieven.sterck3.5k

with inline help, do you mean

bwa mem -help

? I can not find the -K option there, neither in version 0.7.12 nor in 0.7.15...

ADD REPLYlink written 8 weeks ago by gwotto0
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