Hi,
I have been investigating the use of MAQ 0.7.1 for aligning SOLiD reads to a reference and calling SNPs. I am wondering about the behaviour of the -n option which sets maximum mismatches allowed when using maq's map command. MAQ allows only values of 1,2 or 3 for this option. Since in colorspace a SNP is comprised of two adjacent color changes does this mean that reads with more than one SNP cannot be aligned with maq map?
Thanks for any help.
Mr M
I have been investigating the use of MAQ 0.7.1 for aligning SOLiD reads to a reference and calling SNPs. I am wondering about the behaviour of the -n option which sets maximum mismatches allowed when using maq's map command. MAQ allows only values of 1,2 or 3 for this option. Since in colorspace a SNP is comprised of two adjacent color changes does this mean that reads with more than one SNP cannot be aligned with maq map?
Thanks for any help.
Mr M
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