The short answer seems to be 'no' BWA can't do it yet.
(I went through steps like the one here to find that out in the end, the only difference is that I used a modified solid2fastq.pl to process the F5 correctly)
as
bwa sampe
expects the orientation to be the same as SOLiD mate pair
see http://biostar.stackexchange.com/questions/9086/paired-end-mapping-what-is-bwa-solid-paired-end-default-direction-bwa-sampe
while reverse complementing the F5 might work, that itself is problematic due to the colorspace nature of SOLiD reads.
Your options?
Bioscope :(
or bowtie (if you don't need indels) see http://bowtie-bio.sourceforge.net/manual.shtml#paired-end-colorspace-alignment
(I went through steps like the one here to find that out in the end, the only difference is that I used a modified solid2fastq.pl to process the F5 correctly)
as
bwa sampe
expects the orientation to be the same as SOLiD mate pair
see http://biostar.stackexchange.com/questions/9086/paired-end-mapping-what-is-bwa-solid-paired-end-default-direction-bwa-sampe
while reverse complementing the F5 might work, that itself is problematic due to the colorspace nature of SOLiD reads.
Your options?
Bioscope :(
or bowtie (if you don't need indels) see http://bowtie-bio.sourceforge.net/manual.shtml#paired-end-colorspace-alignment
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