> Hi,
>
> From my understanding MAQ is tested for 20-50x coverage regions for SNP
> calling. However, we routinely have projects where depth of coverage
> from Solexa reads is ~5000x.
>
> I see quite a few 'SNPs' that are not called by MAQ.
> These are the duplicate samples, where MAQ does NOT call a SNP
>
> Pos Depth %a %c %g %t
> 64 6632 0.11 92.01 0.69 7.19
> 64 6687 0.07 90.88 0.40 8.64
>
> While for these duplicates it makes a SNP call!
> 64 8594 0.05 91.91 0.54 7.49
> 64 7889 0.13 91.15 0.49 8.23
>
> Any suggestions on what threshold/filter to use to make consistent
> calling with high depth of coverage regions?
>
> From my understanding MAQ is tested for 20-50x coverage regions for SNP
> calling. However, we routinely have projects where depth of coverage
> from Solexa reads is ~5000x.
>
> I see quite a few 'SNPs' that are not called by MAQ.
> These are the duplicate samples, where MAQ does NOT call a SNP
>
> Pos Depth %a %c %g %t
> 64 6632 0.11 92.01 0.69 7.19
> 64 6687 0.07 90.88 0.40 8.64
>
> While for these duplicates it makes a SNP call!
> 64 8594 0.05 91.91 0.54 7.49
> 64 7889 0.13 91.15 0.49 8.23
>
> Any suggestions on what threshold/filter to use to make consistent
> calling with high depth of coverage regions?
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