bwa mem -K 100000000

Question

[gwotto]

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!

[lieven.sterck]

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

Answer 1

[GenoMax]

 -K INT        process INT input bases in each batch regardless of nThreads (for reproducibility) []

It is included in inline help for bwa mem.

[lieven.sterck]

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)

[gwotto]

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...