BWA MEM -K option

Question

[Yihang]

In some alignment scripts, I find that they use the command bwa mem -K 10000000. However, I cannot find any description of the option -K (captial K, not -k). Does anyone know what -K really means?

Thanks!

Answer 1

[Pierre Lindenbaum]

"fixed chunck size" https://github.com/lh3/bwa/blob/139f68fc4c3747813783a488aef2adc86626b01b/fastmap.c#L193C22-L193C38

used in https://github.com/lh3/bwa/blob/master/bwa.c#L79

used in https://github.com/lh3/bwa/blob/master/bwa.c#L104

related to the number of bytes read (fastq) for each iteration

Answer 2

[DBScan]

If I am not mistaken, this flag is usually used for reproducibility reasons.