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Old 01-06-2010, 01:35 PM   #1
johnsequence
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Default percentage of SNP calling in MAQ

How to show directly the percentage of SNP calling in the final.snp file generated from MAQ, that is, how many percent of ATGC in this final SNP report. Fox example, if A (reference) was changed to G (consensus), what is percentage of this G? At the position, maybe 80% of G, 18% of C, 1% of A, and 1% of T. Is there any column we can add in the final report to show these percentage number? Instead of running the MAQ view function that might create a couple hundred GB data, too big.
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Old 01-08-2010, 10:54 AM   #2
apfejes
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I'm currently working on the same problem - I'm not sure there's an answer. A similar question has also been posted to the Maq mailing list, and there doesn't seem to be a reply.

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