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I'm using a Miseq to study low abundance (<5%) somatic mutations. Miseq Reporter doesn't call them although when I look at the data files, they are there.
Illumina says there is a filter in MSR which excludes them and can't be changed.
Does anybody know of a third party software package that will look at the Miseq data files and report these mutations? I have a very reliable reference sequence to use for alignment so no de novo sequencing is required. Seems simple but I can't find the right package.
Alternatively, is there some way to reset the filter (threshold) in MSR?
Many thanks.
LS
Illumina says there is a filter in MSR which excludes them and can't be changed.
Does anybody know of a third party software package that will look at the Miseq data files and report these mutations? I have a very reliable reference sequence to use for alignment so no de novo sequencing is required. Seems simple but I can't find the right package.
Alternatively, is there some way to reset the filter (threshold) in MSR?
Many thanks.
LS