I am interested in testing SOAPsnp on alignments made from from BWA (and other mappers), but SOAPsnp only takes SOAPaligner output format as input. To do this it looks like it is necessary to convert BWA -> SAM -> SOAP.
Can anyone point me to a SAM2SOAP converter?
It looks like this request has been made before in the past on the SOAP google group and SeqAnswers, with no luck. I thought it would be worth trying one more time on BioStar before reinventing the wheel.
Casey and I have made an initial attempt at a SAM->SOAP converter in Python, which can be found on github and is freely available: sam2soap.py
There are two issues:
It's not clear how to translate the Phred-scaled quality scores from the SAM file into SOAP format. My post about this on the BGI-SOAP forum so far hasn't yeilded a response, so for now sam2soap.py just uses the quality scores directly from the input SAM file;
The converter can deal with mutations but it's not obvious how to represent gapped alignments in SOAP format
If someone reading this has more details on either of the above then I'd be delighted to hear from them.
I'm not aware of a SAM->SOAP converter. If it really doesn't exist then I could imagine starting with the reverse conversion for some related insight. For example, the SOAP authors provide this Perl script for SOAP->SAM. Not a very satisfying answer perhaps...
@malachig - more or less when I am planning to do, but thought I'd see if something like this had been done already.
I don't blame you... :)