BWA MEM -K option
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!
• 1,366 views
•
link
2 answers
"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
• 0 views
•
link
If I am not mistaken, this flag is usually used for reproducibility reasons.
• 0 views
•
link
Log in to answer this question.