I am using your program in conjunction with the TASSEL 3 Genotyping By Sequencing Pipeline, which requires the command 'samse' to convert an .sai file to a .sam file. The example command is:
bwa samse referenceSequence/rice.fa mergedTagCounts/myAlignedMasterTags.sai mergedTagCounts/myMasterTags.cnt.fq > mergedTagCounts/myAlignedMasterTags.sam
When I use this command, windows notifies that: 'BWA.exe has stopped working - a problem caused the program to stop working correctly. Windows will close the program and notify you if a solution is available'.
So, I just wanted to check - was the program written such that the samse command is available? Any other thoughts on why this might happen? Sorry if these are really naive questions.
Thanks for your help,
Lisa
Comments: ** Comment from web user: xied75 **
Hi, Lisa and Athi,
Thanks for reporting this issue here.
This is probably due to the difference between versions of BWA. Other people has reported similar behaviour.
The version you download from here has been around for a long time and has been used for real large projects, it's highly unlikely to have any bugs left.
Normally I would suggest you to try run this same command with a Linux machine (on the same version of BWA), if that runs without problem, then it'll confirm the bug in the Windows version; Otherwise, please also try the latest version on Linux.
Currently I have a plan to update the BWA to the latest version; In the meantime, according to a user suggestion, it's possible to compile the latest BWA source with Cygwin 64 bit on Windows, if you managed to get it work, please let me know. :)
Best,
Dong
