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BWA version
To run bwa on SOLiD colorspace data do the following:
1. Create fastq:
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csfastaToFastq -f <in.csfasta> -q <in_QV.qual> -e <experiment name>
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When your csfasta files and quality files are named test_F3.csfasta test_F3_QV.qual, test_F5-RNA.csfasta and test_F5-RNA_QV.qual run:
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solid2fastq_v2.pl test_F3 test_F3.out
solid2fastq_v2.pl test_F5-RNA test_F5-RNA.out
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For some reason, I often have a one bp offset between IGV's view of the genome and BWA's; I fix this by doing math in the parsing of the bwa sampe output:
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awk 'BEGIN {OFS="\t"} {if (substr($1,1,1)=="@") {print $0} else {if ($3!="*") {$4=$4-1; print $0}}}'
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BWA is also installed in Phylocluster