I searched for this discussion but could not find one.
I would like to use only uniquely mapped reads for SNP calling, etc in MAQ. By uniquely mapped I mean, the top hit/best alignment is unique and no other position on reference maps with equally good score. I would want to use only these reads to do SNP calling and further analysis.. I believe its doable using MAQ, but not sure.
Next, I would like to keep track of what reads were dumped because of non-unique mapping, apart from the regular dumped reads found using MAQ's -u option.
I would like to use only uniquely mapped reads for SNP calling, etc in MAQ. By uniquely mapped I mean, the top hit/best alignment is unique and no other position on reference maps with equally good score. I would want to use only these reads to do SNP calling and further analysis.. I believe its doable using MAQ, but not sure.
Next, I would like to keep track of what reads were dumped because of non-unique mapping, apart from the regular dumped reads found using MAQ's -u option.
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